WO2007072975A1 - Method for functionalising a hydrophobic substrate - Google Patents

Method for functionalising a hydrophobic substrate Download PDF

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Publication number
WO2007072975A1
WO2007072975A1 PCT/JP2006/325697 JP2006325697W WO2007072975A1 WO 2007072975 A1 WO2007072975 A1 WO 2007072975A1 JP 2006325697 W JP2006325697 W JP 2006325697W WO 2007072975 A1 WO2007072975 A1 WO 2007072975A1
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WIPO (PCT)
Prior art keywords
peptide
hydrophobic
amino acid
phe
capture agent
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PCT/JP2006/325697
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French (fr)
Inventor
Michael A. Reeve
Sally Anderson
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Sharp Kabushiki Kaisha
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Application filed by Sharp Kabushiki Kaisha filed Critical Sharp Kabushiki Kaisha
Priority to US12/097,574 priority Critical patent/US20090312192A1/en
Priority to EP06843124A priority patent/EP1969370A4/en
Priority to JP2008528695A priority patent/JP4722998B2/en
Publication of WO2007072975A1 publication Critical patent/WO2007072975A1/en

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K17/00—Carrier-bound or immobilised peptides; Preparation thereof
    • C07K17/02—Peptides being immobilised on, or in, an organic carrier
    • C07K17/08—Peptides being immobilised on, or in, an organic carrier the carrier being a synthetic polymer
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K17/00—Carrier-bound or immobilised peptides; Preparation thereof
    • C07K17/14—Peptides being immobilised on, or in, an inorganic carrier
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K7/00—Peptides having 5 to 20 amino acids in a fully defined sequence; Derivatives thereof
    • C07K7/04—Linear peptides containing only normal peptide links
    • C07K7/06—Linear peptides containing only normal peptide links having 5 to 11 amino acids
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K7/00—Peptides having 5 to 20 amino acids in a fully defined sequence; Derivatives thereof
    • C07K7/04—Linear peptides containing only normal peptide links
    • C07K7/08—Linear peptides containing only normal peptide links having 12 to 20 amino acids
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B40/00—Libraries per se, e.g. arrays, mixtures
    • C40B40/04—Libraries containing only organic compounds
    • C40B40/10—Libraries containing peptides or polypeptides, or derivatives thereof
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B50/00—Methods of creating libraries, e.g. combinatorial synthesis
    • C40B50/14—Solid phase synthesis, i.e. wherein one or more library building blocks are bound to a solid support during library creation; Particular methods of cleavage from the solid support
    • C40B50/18—Solid phase synthesis, i.e. wherein one or more library building blocks are bound to a solid support during library creation; Particular methods of cleavage from the solid support using a particular method of attachment to the solid support

Definitions

  • the current invention relates to a novel method for functionalising a hydrophobic substrate, it further relates to capture agents for binding ligands , and it relates to methods of making these capture agents , as well as methods of identifying a capture agent which binds a specific ligand of interest.
  • Pro. SPIE, 4205, 75 (200 1 ) describes the use of cyclohexapeptides bound to quartz surfaces derivatised with epoxides, or directly to gold surfaces. This document describes peptides in which every other amino acid is varied .
  • the peptides are attached to the surfaces by either lysyl or cysteiyl residues. Binding of amino acids to the surface-bound peptides is then assayed .
  • the cyclic peptide worked better than a linear peptide and anchoring by a single lysyl residue worked better than anchoring with three lysyl residues . Binding to volatile organic compounds was assayed using spectroscopic ellipsometry.
  • Crystalline ordering is observed under atomic force microscopy and this appears to be the result of beta- sheet aggregations.
  • alpha helices and beta sheets can be formed from peptides with the same composition yet with different hydrophobic periodicities .
  • Beta sheets can be formed with 7 mers but 14 mers are required in order to produce alpha helices.
  • peptide microarrays and small molecule microarrays are fabricated .
  • Chemoselective ligation can be used with peptides and slide surfaces.
  • An N-terminal cysteiyl residue reacts with an alpha keto aldehyde on the slide surface to give a thiazolidine ring.
  • Others have used the free radical Michael addition between a free thiol and a maleimide . This method cannot be used if there are multiple thiols, as it does not discriminate between them. Journal of the American Chemical Society, 126, 14730 ,
  • a method of functionalising a substrate comprising immobilising at least one multimeric peptide on said substrate , wherein, the at least one multimeric peptide comprises at least first and second peptide chains , said first peptide chain comprising at least one hydrophobic amino acid residue and at least one functionalising moiety, wherein the at least one hydrophobic amino acid residue and at least one functionalising moiety are positioned in the peptide primary structure so as to result in a hydrophobic face, and a substantially non hydrophobic face comprising the functionalising moiety, and wherein contacting the peptide with the substrate causes the peptide to be immobilised thereon .
  • said at least first and second peptide chains are covalently linked to form said multimeric peptide .
  • the substrate is a hydrophobic substrate .
  • the first peptide chain is immobilised on the substrate by a hydrophobic interaction between the substrate and the hydrophobic face of the peptide .
  • the substrate may itself be hydrophobic , such as a hydrophobic material or a hydrophobic solvent, or may be covered in a hydrophobic layer.
  • the substrate is functionalised by self assembly of the peptide on the hydrophobic substrate in the presence of a substantially aqueous solvent.
  • self assembly is driven by entropic effects in the aqueous solvent in contact with the hydrophobic substrate .
  • the hydrophobic amino acid residue is an amino acid selected from the group consisting of L-amino acids, D-amino acids, amino acid mimetics , spacer amino acids, beta amino acids, or any other chiral amino acid monomers.
  • the substantially pure amino acids are L-amino acids and / or D-amino acids.
  • the hydrophobic amino acids whose side chains form the hydrophobic face are selected from the group consisting of leucine , isoleucine, norleucine , valine, norvaline , methionine , tyrosine , tryptophan and phenylalanine . More preferably, the hydrophobic amino acids are phenylalanine .
  • the first peptide chain comprises 4 to 40 hydrophobic amino acid residues, more preferably 6 to 25 and most preferably 6 to 12.
  • each hydrophobic amino acid monomer is substantially enantiomerically pure.
  • the functionalising moiety may comprise any suitable moiety that can be incorporated into peptides using synthesis strategies known to those skilled in the art, for example , it may be selected from hydroxyl groups , thiol groups, carboxylic acids groups , amino groups, amide groups, guanidinium groups, imidazole groups , aromatic groups, chromophores, fluorophores, isotopic labels, chelating groups, haptens , and numerous other moieties.
  • the functionalising moiety comprises at least one amino acid selected from the group comprising L-amino acid s, D-amino acids, amino acid mimetics, spacer amino acids, beta amino acids, or any other chiral amino acid monomers .
  • the amino acids are L-amino acids and/ or D-amino acids.
  • the first peptide chain comprises a primary structure comprising alternating hydrophobic and substantially non hydrophobic amino acid residues as shown in Figure 1 .
  • peptide sequences which result in distribution of the side chains so as to result in a hydrophobic and a substantially non hydrophobic face can be easily designed , for example , there may be three non hydrophobic amino acid residues between hydrophobic residues, or any combination of odd numbers of amino acids.
  • the peptide may comprise a combination of, for example , L- , D- , and beta- amino acids so as to result in a hydrophobic and a substantially non hydrophobic face .
  • each amino acid side chain forming the functionalising moiety is positioned so as to be located on the substantially non hydrophobic face of the first peptide chain and is selected from a set consisting essentially of less than 20 amino acids, more preferably less than 12 amino acids, even more preferably less than 6 amino acids and most preferably 4 amino acids .
  • the first peptide chain comprises 10% to 90% hydrophobic amino acid residues , more preferably, 20% to 80% , even more preferably, 30% to 70%, and most preferably 40% to 60% hydrophobic amino acid residues.
  • the first peptide chain comprises 50% hydrophobic amino acid residues.
  • amino acids whose side chains are positioned on the substantially non hydrophobic face forming the functionalising moiety may also include hydrophobic residues , for example , aminobutyrate residues.
  • the functionalising moiety comprises 10 or fewer amino acid residues whose side chains are located on the substantially non hydrophobic face ; more preferably, 8 or fewer; more preferably, 6 or fewer; even more preferably, 4 or fewer; and most preferably 3 or fewer.
  • the multimeric peptide comprises a peptide dimer comprising first and second peptides.
  • the peptide dimer can be assembled from the first and second peptides before, simultaneously with or after the first peptide has been contacted with the hydrophobic substrate .
  • the peptide dimer is assembled on the hydrophobic substrate .
  • the substrate is derivatised by dispen sing the peptides onto the substrate .
  • the peptides are individually dispensed on to the substrate using a non-contact dispenser, (e . g. Piezorray System, Perkin Elmer LAS) and where they are assembled in situ .
  • a non-contact dispenser e . g. Piezorray System, Perkin Elmer LAS
  • the second peptide chain also comprises at least one hydrophobic amino acid residue and at least one non hydrophobic amino acid residue , wherein said amino acids are positioned in the peptide primary structure such that the amino acid side chains are located to produce a hydrophobic face and a substantially non hydrophobic face comprising the functionalising moiety.
  • the second peptide chain comprises fewer amino acids than the first peptide , and contain s fewer hydrophobic residues such that the interaction between the peptide and the hydrophobic surface is relatively weak.
  • the second peptide chain is only retained on the hydrophobic substrate when dimerised to the first peptide .
  • first and second peptides and the numbers of hydrophobic amino acid residues required to retain them on the substrate will depend upon the hydrophobicity of the surface and on the hydrophobic amino acids present in the first and second peptides, and also on the nature of the ligand to be bound.
  • the amount of peptide retained at the substrate will depend upon the stringency of washing to which the substrate is subjected.
  • the substrate is washed with, for example , 1 .0 M NaCl in 10 mM tris-HCl (pH 8.0) .
  • the second peptide comprises 1 -6 hydrophobic amino acid residues, more preferably, 2 - 5 , and most preferably 2 -4 hydrophobic amino acid residues whose side chains forms the hydrophobic face.
  • the first and second peptides each contain 10 or fewer residue s where side chains are located on the substantially non hydrophobic face functionalising moiety ; more preferably, 8 or fewer; more preferably, 6 or fewer; even more preferably, 4 or fewer; and most preferably 3.
  • the at least first and second peptides can have the same or different primary amino acid sequences.
  • first and second peptides can be synthesised from first and second amino acid sets and that each amino acid set may be the same or different.
  • the peptides are produced from the set of amino acids in a combinatorial manner as is well known in the art.
  • the peptides are produced to a set of rules which may, for example, define the minimum and maximum levels of each amino acid in the peptide, or maximum and minimum levels of the percentage of hydrophobic amino acids incorporated can be provided .
  • the peptides are synthesised on a solid phase , more preferably, the peptides are cleaved from the solid phase prior to use in the method of the first aspect.
  • Peptides may be synthesized using an automated peptide synthesizer (e . g. , a PioneerTM Peptide Synthesizer, Applied Biosystems, Foster City, CA) .
  • a peptide may be prepared on Rink amide resin using FMOC solid phase peptide synthesis followed by trifluoroacetic acid (95%) deprotection and cleavage from the resin .
  • said first and second peptides each contain at least one reactive group .
  • the reactive groups present on the peptides react so as to re sult in the formation of the multimeric capture agent.
  • the reactive groups may be protected during peptide synthesis and deprotected prior to use in production of capture agents according to the first aspect.
  • Such techniques are well known to those skilled in the art, for example , standard FMOC-based solid-phase peptide assembly. In this technique, resin bound peptides with protected side chains and free amino termini are generated . The amino groups at the N-terminus may then be reacted with any compatible carboxylic acid reactive group conj ugate under standard peptide synthesis conditions . For example , cysteine with a trityl or methoxytrityl protected thiol group could be incorporated . Deprotection with trifluoroacetic acid would yield the unprotected peptide in solution .
  • any suitable reaction may be used to form the peptide multimers, for example , Diels Alder reaction between e . g. cyclopentadienyl functionalised peptides and maleimide functionalised peptides, Michael reaction between a thiol functionalised peptide and a maleimide functionalised peptide, reaction between a thiol functionalised peptide and a peptide containing an activated thiol group (activated with for example , a (nitro) thiopyridine moiety) to form a disulfide , Staudinger ligation between an azide functionalised peptide and a phosphinothioester functionalised peptide , and native chemical ligation between a thioester and a N-terminal cysteine .
  • Diels Alder reaction between e . g. cyclopentadienyl functionalised peptides and maleimide functionalised peptides
  • Michael reaction between a
  • the reactive groups may be located in the primary peptide structure of the first and second peptides at any suitable position, for example , the reactive groups may be positioned in the primary peptide sequence such that they are positioned on the substantially non hydrophobic face of the peptides and located on the N-terminal side of the functionalising moiety.
  • the reactive groups may be located in the primary peptide structure of the first and second peptides such that they are positioned on the substantially non hydrophobic face of the peptides, and in the first peptide , on the N-terminal side of the ligand-binding site , and in the second peptide to the C-terminal side of the functionalising moiety.
  • the reactive group may be located in the primary peptide structure of the first and second peptides such that in the first peptide , it is positioned on the substantially non hydrophobic face of the peptide and to the N-terminal side of the functionalising moiety, and in the second peptide it is located on the opposite (hydrophobic) face to the functionalising moiety and to the C-terminal side at this site .
  • the reactive group on the first peptide is located in the primary amino acid structure on the substantially non hydrophobic face and to the N-terminal side of the functionalising moiety and in the second peptide , in the hydrophobic face and to the N-terminal side of the functionalising moiety as shown in Figure 2.
  • said reactive groups are selected from, but not limited to , thiol groups , maleimide , cyclopentadiene , azide , phosphinothioesters , thioesters and (nitro) thiopyridine moiety activated thiols . More preferably, the reactive groups are thiol groups . Preferably, when the reactive groups are thiol groups, at least one thiol group is an activated thiol . Preferably, the thiol group is activated with either a thionitropyridyl or thiopyridyl group.
  • the functionalising moiety allows a ligand to bind to the immobilised peptide .
  • the ligand may be a known molecule , or alternatively, the functionalising moiety may act to bind an unknown molecule.
  • the amino acid side chains may provide a positive charge for ligand-binding.
  • the positive charge is provided by a lysyl residue (four C H2 groups between the peptide chain and the positive charge) , an ornithyl residue (three CH2 groups between the peptide chain and the positive charge) or most preferably, a diaminobutyryl residue (with two CH2 groups between the peptide chain and the positive charge) .
  • the amino acid side chain may alternatively provide a hydroxyl group capable of acting as a hydrogen bond donor and / or acceptor for ligand-binding.
  • the hydroxyl group is provided by a seryl residue (one CH2 group between the peptide chain and the OH group) , or more preferably a homoseryl residue (with two CH2 groups between the peptide chain and the OH group) .
  • the amino acid side chain may provide a hydrophobic moiety for ligand-binding.
  • an alanyl residue no CH2 group between the peptide chain and the methyl group
  • an aminobutyryl residue with one CH2 group between the peptide chain and the methyl group
  • the amino acid side chain may provide a negative charge for ligand-binding.
  • the negative charge is provided by a glutamyl residue (two CH2 groups between the peptide chain and the carboxylate group) , or more preferably, an aspartyl residue (one CH2 group between the peptide chain and the carboxylate group) .
  • the functionalised substrate may comprise multiple immobilised peptides, and that these peptides may be multiple copies of the same peptide , or may comprise multiple different peptides.
  • immobilisation of molecules e . g. peptides
  • the terms " immobilised” and “ attached” are used interchangeably herein and both terms are intended to encompass hydrophobic interactions, unless indicated otherwise , either explicitly or by context. Generally all that is required is that the molecules (e . g. peptides) remain immobilised or attached to the substrate under the conditions in which it is intended to use the substrate , for example in applications requiring peptide ligand-binding.
  • Certain embodiments of the invention may make use of solid supports comprised of an inert substrate or matrix (e.g. glass slides, polymer beads etc) which has been
  • the substrate may be any suitable hydrophobic substrate, for example, gold modified by hydrophobic organic thiol treatment, glass modified by surface treatment, or plastic .
  • the substrate is plastic .
  • the immobilised peptides are arranged in an array on the surface .
  • the array comprises a number of discrete addressable spatially encoded loci .
  • each locus on the array comprises a different immobilised peptide , and more preferably each locus comprises multiple copies of the peptide .
  • multi-peptide arrays distinct regions on the array comprise multiple peptide molecules.
  • each site on the array comprises multiple copies of one individual peptide .
  • Multi-peptide arrays of immobilised peptide molecules may be produced using techniques generally known in the art.
  • bind is intended to encompass direct or indirect, covalent or non-covalent attachment, unless indicated otherwise , either explicitly or by context.
  • covalent attachment may be preferred , but generally all that is required is that the ligands remain bound to the immobilised peptide under the conditions in which it is intended to use the substrate , for example in applications requiring further ligand receptor interactions.
  • a capture agent for binding a ligand comprising at least first and second peptides , the first peptide comprising at least one hydrophobic amino acid residues and at least one ligand-binding moiety, wherein the at least one hydrophobic amino acid residue and at least one ligand-binding moiety are positioned in the peptide primary structure such that the first peptide comprises a hydrophobic face , and a substantially non hydrophobic ligand-binding face .
  • the first and second peptides are covalently linked to form the capture agent.
  • the first peptide comprises a plurality of hydrophobic amino acids .
  • the second peptide comprises 4 to 40 hydrophobic amino acid residues , more preferably 6 to 25 and most preferably 6 to 12.
  • the ligand-binding moiety may comprise any suitable moiety that can be incorporated into peptides using synthesis strategies known to those skilled in the art, for example, it may be selected from hydroxyl groups , thiol groups, carboxylic acids groups, amino groups, amide groups, guanidinium groups, imidazole groups, aromatic groups, chromophores, fluorophores, isotopic labels , chelating groups, haptens, and numerous other moieties.
  • the ligand-binding moiety comprises at least one amino acid . More preferably, the ligand-binding moiety comprises a plurality of amino acids . It will be understood that each amino acid monomer can be an L-amino acid , a D-amino acid , an amino acid mimetic , a spacer amino acid, a beta amino acid, or any other chiral amino acid monomer. Preferably, amino acids are L-amino acids and / or D-amino acids . Preferably, each amino acid monomer is substantially enantiomerically pure .
  • amino acids positioned on the ligand- binding face may also include hydrophobic residue s, for example, aminobutyrate residues.
  • the first peptide comprises a primary structure comprising alternating hydrophobic and non hydrophobic amino acid residues, as shown in Figure 1 .
  • peptide sequences which result in distribution of the side chains so as to result in a hydrophobic and substantially non hydrophobic face can be easily designed , for example , there may be three non hydrophobic amino acid residues between hydrophobic residues, or any combination of odd numbers of amino acid.
  • the peptide may comprise a combination of, for example , L- , D- , and beta- amino acids so as to result a hydrophobic and a substantially non hydrophobic face .
  • each amino acid positioned so that its side chain is located on the ligand-binding face is selected from a set consisting essentially of less than 20 amino acids , more preferably less than 12 amino acids, even more preferably less than 6 amino acids and most preferably 4 amino acids .
  • the first peptide comprises 10% to 90% hydrophobic amino acid residues , more preferably, 20% to 80% , even more preferably, 30% to 70%, and most preferably 40% to 60% hydrophobic amino acid residues.
  • the first peptide comprises 50% hydrophobic amino acid residues .
  • the hydrophobic amino acids which form the hydrophobic face are selected from the group consisting of leucine , isoleucine , norleucine, valine , norvaline , methionine , tyrosine, tryptophan and phenylalanine. More preferably, the hydrophobic amino acids are phenylalanine .
  • the capture agent is located on a hydrophobic substrate such that the substantially non hydrophobic ligand-binding face is accessible for ligand-binding.
  • the capture agent is bound to the hydrophobic substrate by a hydrophobic interaction between the substrate and the hydrophobic face of the first peptide .
  • the substrate may be any suitable hydrophobic substrate , for example, gold modified by hydrophobic organic thiol treatment, glass modified by surface treatment, or plastic.
  • the substrate is plastic .
  • the substrate may be coated in a hydrophobic compound which allows the capture agents to be immobilised thereon in the presence of a substantially aqueous solvent.
  • the capture agent comprises a peptide dimer comprising first and second peptides .
  • the peptide dimer is formed through covalent linkage between the first and second peptides.
  • said peptide dimer is bound to a hydrophobic substrate .
  • the peptide dimer can be assembled from the first and second peptides before, simultaneously with or after the first peptide has been contacted with the hydrophobic substrate.
  • the peptide dimer is assembled on the hydrophobic substrate .
  • the second peptide also comprises at least one hydrophobic amino acid residue and at least one non hydrophobic amino acid residue, wherein said amino acids are positioned in the peptide primary structure such that the amino acid side chains are located in space to produce a hydrophobic face and a substantially non hydrophobic ligand-binding face .
  • the amount of peptide retained at the substrate will depend upon the stringency of washing to which the substrate is subj ected .
  • the substrate is washed with, for example, 1.0 M NaCl in 10 mM tris-HCl (pH 8.0) .
  • the second peptide comprises 1 -6 hydrophobic amino acid residues, more preferably, 2- 5 , and most preferably 2 -4 hydrophobic amino acid residues on the hydrophobic face .
  • the first and second peptides each contain 10 or fewer ligand-binding residues whose side chains are located on the substantially non hydrophobic ligand-binding face; more preferably, 8 or fewer; more preferably, 6 or fewer; even more preferably, 4 or fewer; and most preferably 3 or fewer.
  • the peptides are produced from the set of amino acids in a combinatorial manner as is well known in the art.
  • the peptides are produced to a set of rules which may, for example , define the minimum and maximum levels of each amino acid in the peptide , or the percentage of hydrophobic amino acids incorporated .
  • the first and second peptides are synthesised on a solid phase , more preferably, the peptides are cleaved from the solid phase prior to use in the second aspect.
  • Peptides may be synthesized using an automated peptide synthesizer (e . g. , a PioneerTM Peptide Synthesizer, Applied Biosystems, Foster
  • a peptide may be prepared on Rink amide resin using FMOC solid phase peptide synthesis followed by trifluoroacetic acid (95%) deprotection and cleavage from the resin .
  • the at least first and second peptides can have the same or different primary amino acid sequences.
  • first and second peptides can be synthesised from first and second amino acid sets and that each amino acid set may be the same or different.
  • said first and second peptides each contain at least one reactive group.
  • the reactive groups present on the peptides react so as to result in the formation of a multimeric capture agent.
  • said reactive groups may be protected during peptide synthesis and deprotected prior to use in production of capture agents according to the second aspect.
  • Such techniques are well known to those skilled in the art, for example , standard FMOC-based solid-phase peptide assembly.
  • resin bound peptides with protected side chains and free amino termini are generated .
  • the amino groups at the N-terminus may then be reacted with any compatible carboxylic acid / reactive group conjugate under standard peptide synthesis conditions .
  • cysteine with a trityl or methoxytrityl protected thiol group could be incorporated .
  • Deprotection with trifluoroacetic acid would yield the unprotected peptide in solution .
  • any suitable reaction may be used to form the peptide multimers, for example , Diels Alder reaction between e . g. cyclopentadienyl functionalised peptides and maleimide functionalised peptides , Michael reaction between a thiol functionalised peptide and a maleimide functionalised peptide, reaction between a thiol functionalised peptide and a peptide containing an activated thiol group (activated with, for example , a (nitro) thiopyridine moiety) to form a disulfide, Staudinger ligation between an azide functionalised peptide and a phosphinothioester functionalised peptide, and native chemical ligation between a thioester and a N-terminal cysteine .
  • Diels Alder reaction between e . g. cyclopentadienyl functionalised peptides and maleimide functionalised peptides
  • Michael reaction between a
  • the peptide multimers are formed by disulphide bond formation .
  • the reactive groups may be located in the primary peptide structure of the first and second peptides at any suitable position, for example , the reactive groups may be positioned in the primary peptide sequence such that they are positioned on the substantially non hydrophobic ligand-binding face of the peptides and located on the N-terminal side of the ligand-binding site .
  • the reactive groups may be located in the primary peptide structure of the first and second peptides such that they are positioned on the substantially non hydrophobic ligand-binding face of the peptides and in the first peptide, on the N-terminal side of the ligand-binding site, and in the second peptide to the C- terminal side of the ligand-binding site .
  • the reactive groups may be located in the primary peptide structure of the first and second peptides such that in the first peptide, it is positioned on the substantially non hydrophobic ligand-binding face of the peptides and to the N- terminal side of the ligand-binding site , and in the second peptide it is located on the opposite (hydrophobic) face to the ligand-binding site and to the
  • the reactive group on the first peptide is located in the primary amino acid structure on the substantially non hydrophobic ligand- binding face and to the N-terminal side of the ligand-binding site and in the second peptide , in the hydrophobic face and to the N-terminal side of the ligand-binding site as shown in Figure 2.
  • said reactive groups are selected from, but not limited to , thiol groups, maleimide , cyclopentadiene , azide , phosphinothioesters, thioesters and (nitro) -thiopyridyl activated thiols . More preferably, the reactive groups are thiol groups . Preferably, when the reactive groups are thiol groups, at least one thiol group is an activated thiol . Preferably, the thiol group is activated with either a thionitropyridyl or thiopyridyl group.
  • the capture agents will have different characteristics.
  • the amino acid side chains may provide a positive charge for ligand binding.
  • the positive charge is provided by a lysyl residue (four CH2 groups between the peptide chain and the positive charge) , an ornithyl residue (three C H2 groups between the peptide chain and the positive charge) or most preferably, a diaminobutyryl residue (with two CH2 groups between the peptide chain and the positive charge) .
  • the amino acid may alternatively provide a hydroxyl group capable of acting as a hydrogen bond donor and / or acceptor for ligand binding.
  • the hydroxyl group is provided by a seryl residue (one CH2 group between the peptide chain and the OH group) , or more preferably a homoseryl residue (with two C H2 groups between the peptide chain and the OH group) .
  • the amino acid may provide a hydrophobic moiety for ligand binding.
  • an alanyl residue no CH2 group between the peptide chain and the methyl group
  • an aminobutyryl residue with one CH2 group between the peptide chain and the methyl group
  • the amino acid may provide a negative charge for ligand binding.
  • the negative charge is provided by a glutamyl residue (two C H2 groups between the peptide chain and the carboxylate group) , or more preferably, an aspartyl residue (one CH2 group between the peptide chain and the carboxylate group) .
  • the capture agents of the second aspect are bound to the substrate so as to produce an array. It will be understood that the array may take any convenient form.
  • the method of the invention is applicable to all types of " high density" arrays , including single-molecule arrays .
  • the array comprises a number of discrete addressable spatially encoded loci .
  • each locus on the array comprises a different capture agent, and more preferably each locus comprises multiple copies of the capture agent.
  • the first peptide has the structure set out in SEQ I D No 1 ;
  • CysS(N) P-X'-Phe-Y '-Phe-Z'- Phe where X', Y', and Z' are the ligand-binding residues and CysS (N) P is an activated thiol used for dimer formation (most preferably activated with either a thionitropyridyl group or a thiopyridyl group) .
  • the capture agents according to the second aspect of the current invention are dispensed onto a suitable substrate to form an addressable spatially encoded array of combinatorially varying dimers .
  • the peptides are individually dispensed onto the substrate using a non-contact dispenser, (e . g. Piezorray System, Perkin Elmer LAS) and assembled in situ.
  • a non-contact dispenser e . g. Piezorray System, Perkin Elmer LAS
  • a substrate on which is immobilised at least one capture agent according to the second aspect is provided.
  • a substrate derivatised by the method of the first aspect there is also provided a method of identifying a multimeric capture agent which binds to a ligand of interest, said method comprising producing an array of combinatorial capture agents according to the second aspect, contacting the ligand of interest with the array, and identifying to which capture agent the ligand binds.
  • the binding of the ligand to a capture agent can be identified in various ways known in the art, for example , the ligand or the capture agent may be labelled so that the location on the array to which the ligand binds can be identified.
  • This label may, for example , be a radioactive or fluorescent label using, for example , fluorophores .
  • binding of the ligand of interest to a capture agent may be detected by a variety of other techniques known in the art, for example , calorimetry, absorption spectroscopy, N MR methods , atomic force microscopy and scanning tunnelling microscopy, electrophoresis or chromatography, mass spectroscopy, capillary electrophoresis, surface plasmon resonance detection , surface acoustic wave sensing and numerous microcan tile ver- based approaches.
  • the multimeric capture agents and arrays of multimeric capture agents of the current invention can be used to identify any analyte of choice , since the specific ligand which will be bound by the capture agent will be dependent upon the length and sequence of the peptides from which the capture agent is formed .
  • the ligand comprises a eukaryotic cell, a prokaryotic cell, a virus , a bacteriophage , a prion , a spore , a pollen grain , an allergen , a nucleic acid , a protein , a peptide , a carbohydrate , a lipid , an organic compound , or an inorganic compound .
  • the ligand s are preferably physiological or pharmacological metabolites and most preferably physiological or pharmacological metabolites in human or animal bodily fluids that may be used as diagnostic or prognostic healthcare markers.
  • Figure 1 shows a peptide comprising alternating hydrophobic and non hydrophobic amino acids .
  • Figure 2 shows an example of a dimeric capture agent having a hydrophobic face and a substantially non hydrophobic ligand-binding face .
  • Figure 3 is a graphical representation showing the locations of various hydrophobic peptides in a 96 well plate .
  • Figure 4 shows fluorescence images of the 96 well plate of figure 3 indicating the presence of the various peptides in the wells .
  • Figure 5 shows a graphical repre sentation of the quantified results of the 400V scan of Figure 4.
  • Figure 6A shows fluorescence images indicating the retention of polypeptides P l - I to P l -5 and P2 - 1 to P2 -2 on a polypropylene surface .
  • Figure 6B shows fluorescence images indicating the retention of polypeptides P l - I to P l -5 and P2 - 1 to P2 -2 on a polypropylene surface .
  • Figure 7 shows a graphical representation of the quantified results of Figure 6A,6B .
  • Figure 8 shows fluorescence images indicating the pH resistance of the peptide 2DOS-2 deposited on to a polypropylene hydrophobic surface .
  • Figure 9 shows a graphical representation of the quantified results of the 300V scan of Figure 8.
  • Figure 10 shows fluorescence images indicating the time dependent persistence of the peptide 2DOS-2 deposited on to a polypropylene hydrophobic surface in the presence of an aqueous buffer.
  • Figure 1 1 shows a graphical representation of the results of the 300V scan of Figure 10.
  • Figure 12 is a graphical representation showing the location of various hydrophobic peptides added to flat bottomed and V-bottomed polypropylene 96 well plates.
  • Figure 13 shows fluorescence images of the plates of Figure 10 showing retention of the hydrophobic peptides with and without washing.
  • Figure 14 is a graphical representation of the results of the 500V scan of Figure 13 for the V-bottomed plates.
  • Figure 1 5 is a graphical representation of the results of the 500V scan of Figure 13 for the flat bottomed plates .
  • Figure 16 is a graphical representation showing the location of various hydrophobic peptides added to polypropylene and polystyrene V-bottomed 96 well plates.
  • Figure 17 shows fluorescence images of the plates of Figure 16 showing retention of the hydrophobic peptides with and without washing.
  • Figure 18 is a graphical representation showing the percentage retention of the various peptides in the polypropylene and polystyrene plates of Figure 16 after washing.
  • Figure 19A shows fluorescence images of the microtitre plate from the experiment using the 'liquid phase ' protocol .
  • Figure 19B is a graphical representation of the data from the fluorescence image shown in Table 19.
  • Figure 20A shows fluorescence images of the microtitre plate from the experiment using the 'co-drying' protocol .
  • Figure 2OB is a graphical representation of the data from the fluorescence image shown in Table 22.
  • Figure 2 1 shows fluorescence images indicating the yield of dimer formation on polypropylene sheets .
  • Figure 22 shows a fluorescence images of a 256-element microarray of peptide dimers.
  • spacer amino acid refers to an amino acid, a synthetic amino acid, an amino acid analogue or amino acid mimetic in which the side chains play no part in ligand-binding.
  • capture agent refers to a peptide molecule having a structure such that when a ligand is brought into contact with the capture agent it is bound thereto .
  • multimeric capture agent refers to a capture agent comprising at least two linked subunits
  • peptide refers to a chain comprising 2 or more amino acid residues, synthetic amino acids, amino acid analogues or amino acid mimetics, or any combination thereof.
  • peptide and polypeptide are used interchangeably in this specification .
  • substantially enantiomerically pure indicates that the residue comprise s substantially one type of isomer with any other isomeric forms being there only an impurity.
  • the term located in space in a manner favourable to ligand-binding indicates that the side chains of the peptides which make up the multimeric capture agent are positioned such that they are able to contact and interact with a ligand .
  • substantially non hydrophobic means comprising substantially more hydrophilic residues than hydrophobic residues.
  • residue side chains projecting in front of the plane of the paper represent the combinatorially varied 'ligand-binding face'.
  • the residue side chains projecting behind the plane of the paper represent the 'hydrophobic face' (or negative control residues).
  • Peptides were synthesised on a 2 ⁇ mol scale using standard FMOC chemistry (Alta Bioscience) and were dissolved to 10 ⁇ M in 50% (v/ v) aqueous acetonitrile .
  • microtitre plate was imaged at 200 ⁇ m resolution on a Typhoon Trio Plus variable mode imager (Amersham Biosciences) with the green (532 nm) laser and the 580 BP 30 filter at the PMT voltages indicated below and at normal sensitivity.
  • the scan height was set at +3 mm and the sample was pressed during scanning.
  • the peptides were allowed to evaporate to dryness overnight in the dark and the microtitre plate was again scanned as de scribed above .
  • the fluorescence images were analysed using ImageQuant TL v2003.03 (Amersham Biosciences) .
  • the fluorescence images of the microtitre plate scanned at PMT voltages of 600V, 500V, 400V, and 300V at the three stages of the experiment are shown in Figure 4.
  • Quantification data (using the data from the 400V scan) is given in Table 2 and shown graphically in Figure 5.
  • the polypropylene sheet was wiped with 50% (v/v) aqueous acetonitrile prior to use.
  • the slide was imaged at 10 ⁇ m resolution on a Typhoon Trio Plus variable mode imager (Amersham Biosciences) with the green (532 nm) laser and the 580 BP 30 filter at a PMT voltage of 600 V and at normal sensitivity.
  • the scan height was set at the platen and the samples were pressed during scanning.
  • the fluorescence image was analysed using ImageQuant TL v2003.03 (Amersham Biosciences).
  • the lower half of the slide (containing the test array) was then washed in 100 ml of 1 M NaCl containing 10 mM tris-HCl (pH 8.0) for one minute and were re-scanned as described above .
  • the peptide samples were allowed to evaporate to dryness in the dark.
  • the time-dependent persistence of peptide 2 DOS-2 (see above) deposited onto a polypropylene hydrophobic surface in the presence of aqueous buffer was investigated as shown below: Twelve 100 ⁇ l aliquots of 5 ⁇ M peptide 2 DOS-2 in 5 mM tris- HCl (pH 8.0) in 75% (v / v) aqueous acetonitrile were dispensed to the wells of the top row of a Costar microtitre plate . The peptide samples were allowed to evaporate to dryness in the dark.
  • the dried peptide samples in wells 1 - 10 were incubated with 250 ⁇ l of 1 M NaCl in 1 0 mM tris-H Cl (pH 8.0) for the time indicated below at room temperature . All supernatants were pipetted up and down 8 times after incubation and the supernatants were then removed and placed in the wells of the bottom row of the microtitre plate .
  • the scan height was set at +3 mm and the sample was pressed during scanning.
  • the fluorescence images were analysed using ImageQuant TL v2003.03 (Amersham Biosciences) .
  • Quantification data for peptide 2DOS-2 retention (using data from the 300V scan) are shown in Table 9 and Figure 1 1 .
  • V-bottomed polypropylene microtitre plate and a Greiner flat-bottomed polypropylene microtitre plate according to the following scheme as shown in Figure 12 :
  • the peptide samples were allowed to evaporate to dryness in the dark.
  • peptide samples in the top two rows of the microtitre plates were then incubated for 1 5 minutes at room temperature in 250 ⁇ l of 1 M NaCl in 10 mM tris-HCl (pH 8.0) .
  • wash buffer was pipetted up and down eight times in the well before removing the supernatant.
  • microtitre plates were imaged at 200 ⁇ m resolution on a Typhoon Trio Plus variable mode imager (Amersham Biosciences) with the green (532 nm) laser and the 580 BP 30 filter at the PMT voltages indicated below and at normal sensitivity.
  • the scan height was set at the platen and the sample was pressed during scanning.
  • the fluorescence images were analysed using ImageQuant TL v2003.03 (Amersham Biosciences) .
  • the peptide samples were allowed to evaporate to dryness in the dark.
  • peptide samples in the top two rows of the microtitre plates were then incubated for 1 5 minutes at room temperature in 250 ⁇ l of 1 M NaCl in 10 mM tris- HCl (pH 8.0) . After incubation , the wash buffer was pipetted up and down eight times in the well before removing the supernatant.
  • the washed and untreated peptide samples were then resuspended in 50 ⁇ l of 10 mM tris- HCl (pH 8.0) in 50% (v/ v) aqueous acetonitrile .
  • microtitre plates were imaged at 200 ⁇ m resolution on a Typhoon Trio Plus variable mode imager (Amersham Biosciences) with the green (532 nm) laser and the 580 BP 30 filter at the PMT voltages indicated below and at normal sensitivity.
  • the scan height was set at +3 mm and the sample was pressed during scanning.
  • V-bottom wells (using data from the 400V scan) are given in
  • variable penultimate residue was alanyl , seryl , cysteiyl, or nitropyridylthio activated cysteiyl .
  • TAM RA-labelled fluorescent peptides were also synthesised that contain an N-terminal TAMRA fluorophore attached to a glycyl residue that is attached to a variable C-terminal residue .
  • the variable C-terminal residue was alanyl, seryl, cysteiyl, or nitropyridylthio activated cysteiyl.
  • Example 1 A mixture of the 5-TAMRA and 6-TAMRA isomers as shown in Example 1 was used for the labelling.
  • the full set of eight peptides is shown in Tables 15 and
  • the peptides SB- I to SB-4 and TLSP- I to TLSP-4 were used in order to investigate dimer formation .
  • the SB peptides were mixed with the TLSP peptide s and both were then dried down together onto a polypropylene surface prior to washing the wells and assaying for retained fluorescent material .
  • the microtitre plate was imaged at 200 ⁇ m resolution on a Typhoon Trio Plus variable mode imager (Amersham Biosciences) with the green (532 nm) laser and the 580 BP 30 filter at a PMT voltage of 500 V and at normal sensitivity .
  • the scan height was set at +3 mm and the sample was pressed during scanning.
  • the fluorescence image was analysed using ImageQuant TL v2003.03 (Amersham Biosciences) .
  • the microtitre plate was imaged at 200 ⁇ m resolution on a Typhoon Trio Plus variable mode imager (Amersham Biosciences) with the green (532 nm) laser and the 580 BP 30 filter at a PMT voltage of 500 V and at normal sensitivity .
  • the scan height was set at +3 mm and the sample was pressed during scanning.
  • the fluorescence image was analysed using ImageQuant TL v2003.03 (Amersham Biosciences) .
  • Dimer formation is also observed when the surface peptide possesses an S- nitropyridyl activated thiol group and the solution peptide also possesses an S-nitropyridyl activated thiol group ; when the surface peptide possesses a free thiol group and the solution peptide also possesses a free thiol group; and when the surface peptide possesses an S-nitropyridyl activated thiol group and the solution peptide possesses a free thiol group .
  • Free thiol coupling to free thiols may be due to simple aerobic oxidation , forming disulfide bonds.
  • S-nitropyridyl activated thiol coupling to S-nitropyridyl activated thiols may be a result of incomplete thiol activation , leaving some free thiols able to react with the remaining S-nitropyridyl activated thiols , or some other mechanism.
  • Example 7 peptide dimers are fabricated on a planar plastic surface using a Piezorray (PerkinElmer LAS) non-contact dispenser.
  • the Piezorray (PerkinElmer LAS) is specifically designed for pipetting nanolitre volumes to den se arrays. Liquid volumes are controlled by a piezoelectric tip.
  • the Piezorray system contains a source plate holder, an ultrasonic washbowl, a computer and monitor, and a bottle for system liquid.
  • Polypropylene sheet was obtained from SBA plastics
  • microtitre plate was imaged at 10 ⁇ m resolution on a Typhoon Trio Plus variable mode imager (Amersham
  • the scan height was set at the platen and the sample was pressed during scanning.
  • the fluorescence image was analysed using ImageQuant TL v2003.03 (Amersham
  • the yield of dimer is assayed by the retention of fluorescently labelled peptide that is conditional upon the presence of an unlabelled peptide that can bind to both the polypropylene surface and to the fluorescently labelled peptide .
  • Dimer formation is therefore seen when the surface peptide possesses a free thiol group and the solution peptide possesses an S-nitropyridyl activated thiol group.
  • the simple protocol (without glycerol to prevent evaporation) gives a higher yield of dimer.
  • Example 8 In this example , twenty 256-element microarrays of dimers comprising peptides Ll-Pl-I to 16 and L1-P2-1 to 16 were fabricated in parallel.
  • TCEP tris (2 -carboxyethyl) phosphine Sequence of P l peptides:
  • the fluorescence image for one 18x18 array of dimer and control spots is shown in Figure 22.
  • Fluorescent signal is observable for each Ll-Pl peptide column dispensed to the array. This indicates that each of the Ll-Pl peptides has been successfully dispensed, and is capable of dimer formation. The fluorescent signal is also observable for each L1-P2 peptide row dispensed to the array.
  • the current invention provides synthetic capture agents having increased sequence diversity.
  • the capture agents can functionalize various surfaces , for example , glass or silicon, so as to allow the binding of ligands to the surface , or to form arrays of various types.

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Abstract

The current invention relates to a method of functionalising a substrate comprising immobilising at least one multimeric peptide on the substrate, wherein, the at least one multimeric peptide comprises at least first and second peptide chains, the first peptide chain comprising at least one hydrophobic amino acid residue and at least one functionalising moiety, wherein the at least one hydrophobic amino acid residue and at least one functionalising moiety are positioned in the peptide primary structure so as to result in a hydrophobic face, and a substantially non hydrophobic face comprising the functionalising moiety, and wherein, contacting the peptide with the substrate causes the peptide to be immobilised thereon.

Description

DESCRIPTION
METHOD FOR FUNCTIONALISING A HYDROPHOBIC
SUBSTRATE
TEC H NICAL FIELD The current invention relates to a novel method for functionalising a hydrophobic substrate, it further relates to capture agents for binding ligands , and it relates to methods of making these capture agents , as well as methods of identifying a capture agent which binds a specific ligand of interest.
BACKGROUND ART
The functionalisation of various surfaces , for example , glass or silicon, with diverse molecules so as to allow the binding of ligands to the surface , or to form arrays of various types, is well known .
Pro. SPIE, 4205, 75 (200 1 ) , describes the use of cyclohexapeptides bound to quartz surfaces derivatised with epoxides, or directly to gold surfaces. This document describes peptides in which every other amino acid is varied .
The peptides are attached to the surfaces by either lysyl or cysteiyl residues. Binding of amino acids to the surface-bound peptides is then assayed .
Analytica Chimica Acta, 392 , 2 13 , ( 1999) again describes cyclohexapeptides bound to quartz surfaces derivatised with epoxides . One or three lysyl residues were used for surface anchoring. The cyclic peptide worked better than a linear peptide and anchoring by a single lysyl residue worked better than anchoring with three lysyl residues . Binding to volatile organic compounds was assayed using spectroscopic ellipsometry.
In Angew. Chem . Int. Ed . , 4 1 , 127 , (2002) , Langmuir Blodgett films made from peptides have been investigated using carbon nanotube tipped atomic force microscopy.
Crystalline ordering is observed under atomic force microscopy and this appears to be the result of beta- sheet aggregations.
In J . Am . Chem . Soc , 107, 7684, ( 1985) , lysyl and leucyl residues were used to make peptides of defined conformation at air-water interfaces. These can be transferred to substrates using the Langmuir Blodgett technique . Both alpha helices and beta sheets can be formed from peptides with the same composition yet with different hydrophobic periodicities . Beta sheets can be formed with 7 mers but 14 mers are required in order to produce alpha helices.
In Bioconjugate Chem. , 12 , 346 , (200 1 ) , peptide microarrays and small molecule microarrays are fabricated . Chemoselective ligation can be used with peptides and slide surfaces. An N-terminal cysteiyl residue reacts with an alpha keto aldehyde on the slide surface to give a thiazolidine ring. Others have used the free radical Michael addition between a free thiol and a maleimide . This method cannot be used if there are multiple thiols, as it does not discriminate between them. Journal of the American Chemical Society, 126, 14730 ,
(2004) describes the selective covalent attachment of proteins to surfaces through native chemical ligation . Protein thioesters are reacted with cysteine-derivatised glass surfaces.
DI SCLOSURE OF INVENTION
It is therefore an obj ect of the current invention to provide an alternative method of functionalising a hydrophobic surface . According to a first aspect of the current invention there is provided a method of functionalising a substrate comprising immobilising at least one multimeric peptide on said substrate , wherein, the at least one multimeric peptide comprises at least first and second peptide chains , said first peptide chain comprising at least one hydrophobic amino acid residue and at least one functionalising moiety, wherein the at least one hydrophobic amino acid residue and at least one functionalising moiety are positioned in the peptide primary structure so as to result in a hydrophobic face, and a substantially non hydrophobic face comprising the functionalising moiety, and wherein , contacting the peptide with the substrate causes the peptide to be immobilised thereon .
Preferably, said at least first and second peptide chains are covalently linked to form said multimeric peptide . Preferably, the substrate is a hydrophobic substrate .
Preferably, the first peptide chain is immobilised on the substrate by a hydrophobic interaction between the substrate and the hydrophobic face of the peptide .
It will be understood that the substrate may itself be hydrophobic , such as a hydrophobic material or a hydrophobic solvent, or may be covered in a hydrophobic layer.
Preferably, the substrate is functionalised by self assembly of the peptide on the hydrophobic substrate in the presence of a substantially aqueous solvent. Preferably, self assembly is driven by entropic effects in the aqueous solvent in contact with the hydrophobic substrate .
Preferably, the hydrophobic amino acid residue is an amino acid selected from the group consisting of L-amino acids, D-amino acids, amino acid mimetics , spacer amino acids, beta amino acids, or any other chiral amino acid monomers. Preferably, the substantially pure amino acids are L-amino acids and / or D-amino acids.
Preferably, the hydrophobic amino acids whose side chains form the hydrophobic face are selected from the group consisting of leucine , isoleucine, norleucine , valine, norvaline , methionine , tyrosine , tryptophan and phenylalanine . More preferably, the hydrophobic amino acids are phenylalanine . Preferably, the first peptide chain comprises 4 to 40 hydrophobic amino acid residues, more preferably 6 to 25 and most preferably 6 to 12.
Preferably, each hydrophobic amino acid monomer is substantially enantiomerically pure. It will be understood that the functionalising moiety may comprise any suitable moiety that can be incorporated into peptides using synthesis strategies known to those skilled in the art, for example , it may be selected from hydroxyl groups , thiol groups, carboxylic acids groups , amino groups, amide groups, guanidinium groups, imidazole groups , aromatic groups, chromophores, fluorophores, isotopic labels, chelating groups, haptens , and numerous other moieties.
Preferably, the functionalising moiety comprises at least one amino acid selected from the group comprising L-amino acid s, D-amino acids, amino acid mimetics, spacer amino acids, beta amino acids, or any other chiral amino acid monomers . Preferably, the amino acids are L-amino acids and/ or D-amino acids.
Preferably, each amino acid monomer whose side chain forms the functionalising moiety is substantially enantiomerically pure .
Preferably, the first peptide chain comprises a primary structure comprising alternating hydrophobic and substantially non hydrophobic amino acid residues as shown in Figure 1 .
It will be understood by the skilled person that other peptide sequences which result in distribution of the side chains so as to result in a hydrophobic and a substantially non hydrophobic face can be easily designed , for example , there may be three non hydrophobic amino acid residues between hydrophobic residues, or any combination of odd numbers of amino acids. Alternatively, the peptide may comprise a combination of, for example , L- , D- , and beta- amino acids so as to result in a hydrophobic and a substantially non hydrophobic face .
In a preferred embodiment, each amino acid side chain forming the functionalising moiety is positioned so as to be located on the substantially non hydrophobic face of the first peptide chain and is selected from a set consisting essentially of less than 20 amino acids, more preferably less than 12 amino acids, even more preferably less than 6 amino acids and most preferably 4 amino acids .
Preferably, the first peptide chain comprises 10% to 90% hydrophobic amino acid residues , more preferably, 20% to 80% , even more preferably, 30% to 70%, and most preferably 40% to 60% hydrophobic amino acid residues.
In a particularly preferred embodiment, the first peptide chain comprises 50% hydrophobic amino acid residues.
It will be understood that amino acids whose side chains are positioned on the substantially non hydrophobic face forming the functionalising moiety may also include hydrophobic residues , for example , aminobutyrate residues.
Preferably, the functionalising moiety comprises 10 or fewer amino acid residues whose side chains are located on the substantially non hydrophobic face ; more preferably, 8 or fewer; more preferably, 6 or fewer; even more preferably, 4 or fewer; and most preferably 3 or fewer.
Preferably, the multimeric peptide comprises a peptide dimer comprising first and second peptides. I t will be apparent that the peptide dimer can be assembled from the first and second peptides before, simultaneously with or after the first peptide has been contacted with the hydrophobic substrate . In a particularly preferred embodiment, the peptide dimer is assembled on the hydrophobic substrate .
In the most preferred embodiment, the substrate is derivatised by dispen sing the peptides onto the substrate .
Preferably, the peptides are individually dispensed on to the substrate using a non-contact dispenser, (e . g. Piezorray System, Perkin Elmer LAS) and where they are assembled in situ .
Preferably, the second peptide chain also comprises at least one hydrophobic amino acid residue and at least one non hydrophobic amino acid residue , wherein said amino acids are positioned in the peptide primary structure such that the amino acid side chains are located to produce a hydrophobic face and a substantially non hydrophobic face comprising the functionalising moiety.
In a preferred embodiment, the second peptide chain comprises fewer amino acids than the first peptide , and contain s fewer hydrophobic residues such that the interaction between the peptide and the hydrophobic surface is relatively weak. In this embodiment, the second peptide chain is only retained on the hydrophobic substrate when dimerised to the first peptide .
It will be apparent to the skilled person that the length of the first and second peptides and the numbers of hydrophobic amino acid residues required to retain them on the substrate will depend upon the hydrophobicity of the surface and on the hydrophobic amino acids present in the first and second peptides, and also on the nature of the ligand to be bound.
It will also be readily apparent to the skilled person that the amount of peptide retained at the substrate will depend upon the stringency of washing to which the substrate is subjected. Preferably, after immobilisation of the peptides, the substrate is washed with, for example , 1 .0 M NaCl in 10 mM tris-HCl (pH 8.0) .
Preferably, the second peptide comprises 1 -6 hydrophobic amino acid residues, more preferably, 2 - 5 , and most preferably 2 -4 hydrophobic amino acid residues whose side chains forms the hydrophobic face.
Preferably, the first and second peptides each contain 10 or fewer residue s where side chains are located on the substantially non hydrophobic face functionalising moiety ; more preferably, 8 or fewer; more preferably, 6 or fewer; even more preferably, 4 or fewer; and most preferably 3.
It will be readily apparent that the at least first and second peptides can have the same or different primary amino acid sequences.
It will be further apparent that the first and second peptides can be synthesised from first and second amino acid sets and that each amino acid set may be the same or different. Preferably, the peptides are produced from the set of amino acids in a combinatorial manner as is well known in the art.
In a preferred embodiment, the peptides are produced to a set of rules which may, for example, define the minimum and maximum levels of each amino acid in the peptide, or maximum and minimum levels of the percentage of hydrophobic amino acids incorporated can be provided .
Preferably, the peptides are synthesised on a solid phase , more preferably, the peptides are cleaved from the solid phase prior to use in the method of the first aspect.
Syntheses of peptides and their salts and derivatives , including both solid phase and solution phase peptide syntheses, are well established in the art. See , e . g. , Stewart, et al . ( 1984) Solid Phase Peptide Synthesis (2nd Ed . ) ; and Chan (2000) "FMOC Solid Phase Peptide Synthesis , A
Practical Approach," Oxford University Press. Peptides may be synthesized using an automated peptide synthesizer (e . g. , a Pioneer™ Peptide Synthesizer, Applied Biosystems, Foster City, CA) . For example , a peptide may be prepared on Rink amide resin using FMOC solid phase peptide synthesis followed by trifluoroacetic acid (95%) deprotection and cleavage from the resin .
Preferably, said first and second peptides each contain at least one reactive group . In a preferred embodiment, the reactive groups present on the peptides react so as to re sult in the formation of the multimeric capture agent.
In a preferred embodiment, the reactive groups may be protected during peptide synthesis and deprotected prior to use in production of capture agents according to the first aspect. Such techniques are well known to those skilled in the art, for example , standard FMOC-based solid-phase peptide assembly. In this technique, resin bound peptides with protected side chains and free amino termini are generated . The amino groups at the N-terminus may then be reacted with any compatible carboxylic acid reactive group conj ugate under standard peptide synthesis conditions . For example , cysteine with a trityl or methoxytrityl protected thiol group could be incorporated . Deprotection with trifluoroacetic acid would yield the unprotected peptide in solution .
It will be understood that any suitable reaction may be used to form the peptide multimers, for example , Diels Alder reaction between e . g. cyclopentadienyl functionalised peptides and maleimide functionalised peptides, Michael reaction between a thiol functionalised peptide and a maleimide functionalised peptide, reaction between a thiol functionalised peptide and a peptide containing an activated thiol group (activated with for example , a (nitro) thiopyridine moiety) to form a disulfide , Staudinger ligation between an azide functionalised peptide and a phosphinothioester functionalised peptide , and native chemical ligation between a thioester and a N-terminal cysteine .
It will be understood that the reactive groups may be located in the primary peptide structure of the first and second peptides at any suitable position, for example , the reactive groups may be positioned in the primary peptide sequence such that they are positioned on the substantially non hydrophobic face of the peptides and located on the N-terminal side of the functionalising moiety. Alternatively, the reactive groups may be located in the primary peptide structure of the first and second peptides such that they are positioned on the substantially non hydrophobic face of the peptides, and in the first peptide , on the N-terminal side of the ligand-binding site , and in the second peptide to the C-terminal side of the functionalising moiety.
In a further embodiment, the reactive group may be located in the primary peptide structure of the first and second peptides such that in the first peptide , it is positioned on the substantially non hydrophobic face of the peptide and to the N-terminal side of the functionalising moiety, and in the second peptide it is located on the opposite (hydrophobic) face to the functionalising moiety and to the C-terminal side at this site . In a preferred embodiment, the reactive group on the first peptide is located in the primary amino acid structure on the substantially non hydrophobic face and to the N-terminal side of the functionalising moiety and in the second peptide , in the hydrophobic face and to the N-terminal side of the functionalising moiety as shown in Figure 2. Preferably , said reactive groups are selected from, but not limited to , thiol groups , maleimide , cyclopentadiene , azide , phosphinothioesters , thioesters and (nitro) thiopyridine moiety activated thiols . More preferably, the reactive groups are thiol groups . Preferably, when the reactive groups are thiol groups, at least one thiol group is an activated thiol . Preferably, the thiol group is activated with either a thionitropyridyl or thiopyridyl group.
Preferably, the functionalising moiety allows a ligand to bind to the immobilised peptide .
It will be apparent that the ligand may be a known molecule , or alternatively, the functionalising moiety may act to bind an unknown molecule.
It will further be apparent that, depending upon the amino acid residues present in the peptides , the functionalising moiety will have different characteristics.
For example, the amino acid side chains may provide a positive charge for ligand-binding. Preferably, the positive charge is provided by a lysyl residue (four C H2 groups between the peptide chain and the positive charge) , an ornithyl residue (three CH2 groups between the peptide chain and the positive charge) or most preferably, a diaminobutyryl residue (with two CH2 groups between the peptide chain and the positive charge) . The amino acid side chain may alternatively provide a hydroxyl group capable of acting as a hydrogen bond donor and / or acceptor for ligand-binding. Preferably, the hydroxyl group is provided by a seryl residue (one CH2 group between the peptide chain and the OH group) , or more preferably a homoseryl residue (with two CH2 groups between the peptide chain and the OH group) .
The amino acid side chain may provide a hydrophobic moiety for ligand-binding. Preferably, an alanyl residue (no CH2 group between the peptide chain and the methyl group) or more preferably, an aminobutyryl residue (with one CH2 group between the peptide chain and the methyl group) provides the hydrophobic moiety.
Alternatively, the amino acid side chain may provide a negative charge for ligand-binding. Preferably, the negative charge is provided by a glutamyl residue (two CH2 groups between the peptide chain and the carboxylate group) , or more preferably, an aspartyl residue (one CH2 group between the peptide chain and the carboxylate group) .
It will further be apparent that the functionalised substrate may comprise multiple immobilised peptides, and that these peptides may be multiple copies of the same peptide , or may comprise multiple different peptides.
When referring to immobilisation of molecules (e . g. peptides) to a substrate , the terms " immobilised" and " attached" are used interchangeably herein and both terms are intended to encompass hydrophobic interactions, unless indicated otherwise , either explicitly or by context. Generally all that is required is that the molecules (e . g. peptides) remain immobilised or attached to the substrate under the conditions in which it is intended to use the substrate , for example in applications requiring peptide ligand-binding.
Certain embodiments of the invention may make use of solid supports comprised of an inert substrate or matrix (e.g. glass slides, polymer beads etc) which has been
"functionalised" , for example by application of a layer or coating of an intermediate material comprising reactive groups which permit hydrophobic attachment of biomolecules such as peptides. It will be understood that the substrate may be any suitable hydrophobic substrate, for example, gold modified by hydrophobic organic thiol treatment, glass modified by surface treatment, or plastic . Preferably, the substrate is plastic . Preferably, the immobilised peptides are arranged in an array on the surface . Preferably, the array comprises a number of discrete addressable spatially encoded loci . Preferably, each locus on the array comprises a different immobilised peptide , and more preferably each locus comprises multiple copies of the peptide . In multi-peptide arrays, distinct regions on the array comprise multiple peptide molecules. Preferably, each site on the array comprises multiple copies of one individual peptide . Multi-peptide arrays of immobilised peptide molecules may be produced using techniques generally known in the art.
When referring to binding of ligands to the immobilised peptides, the term bind is intended to encompass direct or indirect, covalent or non-covalent attachment, unless indicated otherwise , either explicitly or by context. In certain embodiments of the invention , covalent attachment may be preferred , but generally all that is required is that the ligands remain bound to the immobilised peptide under the conditions in which it is intended to use the substrate , for example in applications requiring further ligand receptor interactions.
According to a second aspect of the current invention there is provided a capture agent for binding a ligand , comprising at least first and second peptides , the first peptide comprising at least one hydrophobic amino acid residues and at least one ligand-binding moiety, wherein the at least one hydrophobic amino acid residue and at least one ligand-binding moiety are positioned in the peptide primary structure such that the first peptide comprises a hydrophobic face , and a substantially non hydrophobic ligand-binding face .
Preferably, the first and second peptides are covalently linked to form the capture agent.
Preferably, the first peptide comprises a plurality of hydrophobic amino acids .
Preferably, the second peptide comprises 4 to 40 hydrophobic amino acid residues , more preferably 6 to 25 and most preferably 6 to 12.
It will be understood that the ligand-binding moiety may comprise any suitable moiety that can be incorporated into peptides using synthesis strategies known to those skilled in the art, for example, it may be selected from hydroxyl groups , thiol groups, carboxylic acids groups, amino groups, amide groups, guanidinium groups, imidazole groups, aromatic groups, chromophores, fluorophores, isotopic labels , chelating groups, haptens, and numerous other moieties.
Preferably, the ligand-binding moiety comprises at least one amino acid . More preferably, the ligand-binding moiety comprises a plurality of amino acids . It will be understood that each amino acid monomer can be an L-amino acid , a D-amino acid , an amino acid mimetic , a spacer amino acid, a beta amino acid, or any other chiral amino acid monomer. Preferably, amino acids are L-amino acids and / or D-amino acids . Preferably, each amino acid monomer is substantially enantiomerically pure .
It will be understood that amino acids positioned on the ligand- binding face may also include hydrophobic residue s, for example, aminobutyrate residues. Preferably, the first peptide comprises a primary structure comprising alternating hydrophobic and non hydrophobic amino acid residues, as shown in Figure 1 .
It will be understood by the skilled person that other peptide sequences which result in distribution of the side chains so as to result in a hydrophobic and substantially non hydrophobic face can be easily designed , for example , there may be three non hydrophobic amino acid residues between hydrophobic residues, or any combination of odd numbers of amino acid. Alternatively, the peptide may comprise a combination of, for example , L- , D- , and beta- amino acids so as to result a hydrophobic and a substantially non hydrophobic face .
Preferably, each amino acid positioned so that its side chain is located on the ligand-binding face is selected from a set consisting essentially of less than 20 amino acids , more preferably less than 12 amino acids, even more preferably less than 6 amino acids and most preferably 4 amino acids .
Preferably, the first peptide comprises 10% to 90% hydrophobic amino acid residues , more preferably, 20% to 80% , even more preferably, 30% to 70%, and most preferably 40% to 60% hydrophobic amino acid residues.
In a particularly preferred embodiment, the first peptide comprises 50% hydrophobic amino acid residues .
Preferably, the hydrophobic amino acids which form the hydrophobic face are selected from the group consisting of leucine , isoleucine , norleucine, valine , norvaline , methionine , tyrosine, tryptophan and phenylalanine. More preferably, the hydrophobic amino acids are phenylalanine .
In a preferred embodiment, the capture agent is located on a hydrophobic substrate such that the substantially non hydrophobic ligand-binding face is accessible for ligand-binding.
Preferably, the capture agent is bound to the hydrophobic substrate by a hydrophobic interaction between the substrate and the hydrophobic face of the first peptide .
It will be understood that the substrate may be any suitable hydrophobic substrate , for example, gold modified by hydrophobic organic thiol treatment, glass modified by surface treatment, or plastic. Preferably, the substrate is plastic .
Alternatively, the substrate may be coated in a hydrophobic compound which allows the capture agents to be immobilised thereon in the presence of a substantially aqueous solvent. Preferably, the capture agent comprises a peptide dimer comprising first and second peptides .
More preferably, the peptide dimer is formed through covalent linkage between the first and second peptides.
Preferably, said peptide dimer is bound to a hydrophobic substrate . It will be apparent that the peptide dimer can be assembled from the first and second peptides before, simultaneously with or after the first peptide has been contacted with the hydrophobic substrate. In a particularly preferred embodiment, the peptide dimer is assembled on the hydrophobic substrate .
Preferably, the second peptide also comprises at least one hydrophobic amino acid residue and at least one non hydrophobic amino acid residue, wherein said amino acids are positioned in the peptide primary structure such that the amino acid side chains are located in space to produce a hydrophobic face and a substantially non hydrophobic ligand-binding face .
Preferably, the second peptide comprises a plurality of non hydrophobic amino acid residues . In a preferred embodiment, the second peptide comprises fewer amino acids than the first peptide, and contains fewer hydrophobic residues such that the interaction between the peptide and the hydrophobic surface is relatively weak. In this embodiment, the second peptide is only retained on the hydrophobic substrate when dimerised to the first peptide .
I t will be apparent to the skilled person that length of the first and second peptides and the numbers of hydrophobic amino acid residues required to retain them on the substrate will depend upon the hydrophobicity of the surface and on the hydrophobic amino acids present in the first and second peptides, and also on the nature of the ligand to be bound .
It will also be readily apparent to the skilled person that the amount of peptide retained at the substrate will depend upon the stringency of washing to which the substrate is subj ected . Preferably, after immobilisation of the peptides, the substrate is washed with, for example, 1.0 M NaCl in 10 mM tris-HCl (pH 8.0) .
Preferably, the second peptide comprises 1 -6 hydrophobic amino acid residues, more preferably, 2- 5 , and most preferably 2 -4 hydrophobic amino acid residues on the hydrophobic face .
Preferably, the first and second peptides each contain 10 or fewer ligand-binding residues whose side chains are located on the substantially non hydrophobic ligand-binding face; more preferably, 8 or fewer; more preferably, 6 or fewer; even more preferably, 4 or fewer; and most preferably 3 or fewer.
Preferably, the peptides are produced from the set of amino acids in a combinatorial manner as is well known in the art.
In a preferred embodiment, the peptides are produced to a set of rules which may, for example , define the minimum and maximum levels of each amino acid in the peptide , or the percentage of hydrophobic amino acids incorporated .
Preferably, the first and second peptides are synthesised on a solid phase , more preferably, the peptides are cleaved from the solid phase prior to use in the second aspect.
Syntheses of peptides and their salts and derivatives, including both solid phase and solution phase peptide syntheses, are well established in the art. See , e . g. , Stewart, et al . ( 1984) Solid Phase Peptide Synthesis (2nd Ed . ) ; and
Chan (2000) "FMOC Solid Phase Peptide Synthesis , A
Practical Approach ," Oxford University Press . Peptides may be synthesized using an automated peptide synthesizer (e . g. , a Pioneer™ Peptide Synthesizer, Applied Biosystems, Foster
City, CA) . For example , a peptide may be prepared on Rink amide resin using FMOC solid phase peptide synthesis followed by trifluoroacetic acid (95%) deprotection and cleavage from the resin .
It will be readily apparent that the at least first and second peptides can have the same or different primary amino acid sequences.
It will be further apparent that the first and second peptides can be synthesised from first and second amino acid sets and that each amino acid set may be the same or different.
Preferably, said first and second peptides each contain at least one reactive group. In a preferred embodiment, the reactive groups present on the peptides react so as to result in the formation of a multimeric capture agent.
In a preferred embodiment, said reactive groups may be protected during peptide synthesis and deprotected prior to use in production of capture agents according to the second aspect. Such techniques are well known to those skilled in the art, for example , standard FMOC-based solid-phase peptide assembly. In this technique , resin bound peptides with protected side chains and free amino termini are generated . The amino groups at the N-terminus may then be reacted with any compatible carboxylic acid / reactive group conjugate under standard peptide synthesis conditions . For example , cysteine with a trityl or methoxytrityl protected thiol group could be incorporated . Deprotection with trifluoroacetic acid would yield the unprotected peptide in solution .
It will be understood that any suitable reaction may be used to form the peptide multimers, for example , Diels Alder reaction between e . g. cyclopentadienyl functionalised peptides and maleimide functionalised peptides , Michael reaction between a thiol functionalised peptide and a maleimide functionalised peptide, reaction between a thiol functionalised peptide and a peptide containing an activated thiol group (activated with, for example , a (nitro) thiopyridine moiety) to form a disulfide, Staudinger ligation between an azide functionalised peptide and a phosphinothioester functionalised peptide, and native chemical ligation between a thioester and a N-terminal cysteine . In a preferred embodiment, the peptide multimers are formed by disulphide bond formation . It will be understood that the reactive groups may be located in the primary peptide structure of the first and second peptides at any suitable position, for example , the reactive groups may be positioned in the primary peptide sequence such that they are positioned on the substantially non hydrophobic ligand-binding face of the peptides and located on the N-terminal side of the ligand-binding site .
Alternatively, the reactive groups may be located in the primary peptide structure of the first and second peptides such that they are positioned on the substantially non hydrophobic ligand-binding face of the peptides and in the first peptide, on the N-terminal side of the ligand-binding site, and in the second peptide to the C- terminal side of the ligand-binding site .
In a further embodiment, the reactive groups may be located in the primary peptide structure of the first and second peptides such that in the first peptide, it is positioned on the substantially non hydrophobic ligand-binding face of the peptides and to the N- terminal side of the ligand-binding site , and in the second peptide it is located on the opposite (hydrophobic) face to the ligand-binding site and to the
C-terminal side of the ligand-binding site .
In a preferred embodiment, the reactive group on the first peptide is located in the primary amino acid structure on the substantially non hydrophobic ligand- binding face and to the N-terminal side of the ligand-binding site and in the second peptide , in the hydrophobic face and to the N-terminal side of the ligand-binding site as shown in Figure 2.
Preferably, said reactive groups are selected from, but not limited to , thiol groups, maleimide , cyclopentadiene , azide , phosphinothioesters, thioesters and (nitro) -thiopyridyl activated thiols . More preferably, the reactive groups are thiol groups . Preferably, when the reactive groups are thiol groups, at least one thiol group is an activated thiol . Preferably, the thiol group is activated with either a thionitropyridyl or thiopyridyl group.
It will be apparent that, depending upon the amino acid residues present in the peptides, the capture agents will have different characteristics. For example , the amino acid side chains may provide a positive charge for ligand binding. Preferably, the positive charge is provided by a lysyl residue (four CH2 groups between the peptide chain and the positive charge) , an ornithyl residue (three C H2 groups between the peptide chain and the positive charge) or most preferably, a diaminobutyryl residue (with two CH2 groups between the peptide chain and the positive charge) .
The amino acid may alternatively provide a hydroxyl group capable of acting as a hydrogen bond donor and / or acceptor for ligand binding. Preferably , the hydroxyl group is provided by a seryl residue (one CH2 group between the peptide chain and the OH group) , or more preferably a homoseryl residue (with two C H2 groups between the peptide chain and the OH group) .
The amino acid may provide a hydrophobic moiety for ligand binding. Preferably, an alanyl residue (no CH2 group between the peptide chain and the methyl group) or more preferably, an aminobutyryl residue (with one CH2 group between the peptide chain and the methyl group) provides the hydrophobic moiety.
Alternatively , the amino acid may provide a negative charge for ligand binding. Preferably, the negative charge is provided by a glutamyl residue (two C H2 groups between the peptide chain and the carboxylate group) , or more preferably, an aspartyl residue (one CH2 group between the peptide chain and the carboxylate group) . Preferably, the capture agents of the second aspect are bound to the substrate so as to produce an array. It will be understood that the array may take any convenient form. Thus , the method of the invention is applicable to all types of " high density" arrays , including single-molecule arrays . Preferably, the array comprises a number of discrete addressable spatially encoded loci . Preferably, each locus on the array comprises a different capture agent, and more preferably each locus comprises multiple copies of the capture agent. In a particularly preferred embodiment, the first peptide has the structure set out in SEQ I D No 1 ;
(Phe-Glyjn-Phe-Cys-Phe-X-Phe-Y-Phe-Z-Phe-Gly-Phe where X, Y, and Z are the ligand-binding residues and Cys provides a nucleophilic thiol used for dimer formation. The second peptide has the preferred structure set out in SEQ I D No 2 ;
CysS(N) P-X'-Phe-Y '-Phe-Z'- Phe where X', Y', and Z' are the ligand-binding residues and CysS (N) P is an activated thiol used for dimer formation (most preferably activated with either a thionitropyridyl group or a thiopyridyl group) .
It is to be understood that the preceding preferred embodiment is by way of example only and is not to be taken to be limiting. It will be apparent to the skilled person that many other reactive groups and activating groups can be employed in the current invention .
In the most preferred embodiment, the capture agents according to the second aspect of the current invention are dispensed onto a suitable substrate to form an addressable spatially encoded array of combinatorially varying dimers .
Preferably, the peptides are individually dispensed onto the substrate using a non-contact dispenser, (e . g. Piezorray System, Perkin Elmer LAS) and assembled in situ.
According to a third aspect of the present invention , there is provided a substrate on which is immobilised at least one capture agent according to the second aspect.
According to a fourth aspect of the present invention , there is also provided a substrate derivatised by the method of the first aspect. According to the present invention , there is also provided a method of identifying a multimeric capture agent which binds to a ligand of interest, said method comprising producing an array of combinatorial capture agents according to the second aspect, contacting the ligand of interest with the array, and identifying to which capture agent the ligand binds.
It will be apparent to the skilled person that the binding of the ligand to a capture agent can be identified in various ways known in the art, for example , the ligand or the capture agent may be labelled so that the location on the array to which the ligand binds can be identified. This label may, for example , be a radioactive or fluorescent label using, for example , fluorophores . Alternatively, binding of the ligand of interest to a capture agent may be detected by a variety of other techniques known in the art, for example , calorimetry, absorption spectroscopy, N MR methods , atomic force microscopy and scanning tunnelling microscopy, electrophoresis or chromatography, mass spectroscopy, capillary electrophoresis, surface plasmon resonance detection , surface acoustic wave sensing and numerous microcan tile ver- based approaches.
It will be understood that the multimeric capture agents and arrays of multimeric capture agents of the current invention can be used to identify any analyte of choice , since the specific ligand which will be bound by the capture agent will be dependent upon the length and sequence of the peptides from which the capture agent is formed . In preferred embodiments, the ligand comprises a eukaryotic cell, a prokaryotic cell, a virus , a bacteriophage , a prion , a spore , a pollen grain , an allergen , a nucleic acid , a protein , a peptide , a carbohydrate , a lipid , an organic compound , or an inorganic compound . The ligand s are preferably physiological or pharmacological metabolites and most preferably physiological or pharmacological metabolites in human or animal bodily fluids that may be used as diagnostic or prognostic healthcare markers.
Additional obj ects, features , and strengths of the present invention will be made clear by the description below.
Further, the advantages of the present invention will be evident from the following explanation in reference to the drawings.
BRI EF DESC RIPTION OF DRAWI NGS
The invention will be further understood with reference to the following experimental examples and accompanying figures in which : -
Figure 1 shows a peptide comprising alternating hydrophobic and non hydrophobic amino acids . Figure 2 shows an example of a dimeric capture agent having a hydrophobic face and a substantially non hydrophobic ligand-binding face .
Figure 3 is a graphical representation showing the locations of various hydrophobic peptides in a 96 well plate . Figure 4 shows fluorescence images of the 96 well plate of figure 3 indicating the presence of the various peptides in the wells .
Figure 5 shows a graphical repre sentation of the quantified results of the 400V scan of Figure 4. Figure 6A shows fluorescence images indicating the retention of polypeptides P l - I to P l -5 and P2 - 1 to P2 -2 on a polypropylene surface .
Figure 6B shows fluorescence images indicating the retention of polypeptides P l - I to P l -5 and P2 - 1 to P2 -2 on a polypropylene surface .
Figure 7 shows a graphical representation of the quantified results of Figure 6A,6B .
Figure 8 shows fluorescence images indicating the pH resistance of the peptide 2DOS-2 deposited on to a polypropylene hydrophobic surface .
Figure 9 shows a graphical representation of the quantified results of the 300V scan of Figure 8.
Figure 10 shows fluorescence images indicating the time dependent persistence of the peptide 2DOS-2 deposited on to a polypropylene hydrophobic surface in the presence of an aqueous buffer.
Figure 1 1 shows a graphical representation of the results of the 300V scan of Figure 10.
Figure 12 is a graphical representation showing the location of various hydrophobic peptides added to flat bottomed and V-bottomed polypropylene 96 well plates.
Figure 13 shows fluorescence images of the plates of Figure 10 showing retention of the hydrophobic peptides with and without washing. Figure 14 is a graphical representation of the results of the 500V scan of Figure 13 for the V-bottomed plates.
Figure 1 5 is a graphical representation of the results of the 500V scan of Figure 13 for the flat bottomed plates .
Figure 16 is a graphical representation showing the location of various hydrophobic peptides added to polypropylene and polystyrene V-bottomed 96 well plates.
Figure 17 shows fluorescence images of the plates of Figure 16 showing retention of the hydrophobic peptides with and without washing. Figure 18 is a graphical representation showing the percentage retention of the various peptides in the polypropylene and polystyrene plates of Figure 16 after washing.
Figure 19A shows fluorescence images of the microtitre plate from the experiment using the 'liquid phase ' protocol .
Figure 19B is a graphical representation of the data from the fluorescence image shown in Table 19.
Figure 20A shows fluorescence images of the microtitre plate from the experiment using the 'co-drying' protocol . Figure 2OB is a graphical representation of the data from the fluorescence image shown in Table 22.
Figure 2 1 shows fluorescence images indicating the yield of dimer formation on polypropylene sheets .
Figure 22 shows a fluorescence images of a 256-element microarray of peptide dimers. BEST MODE FOR CARRYING OUT THE INVENTION
As used herein , the term spacer amino acid refers to an amino acid, a synthetic amino acid, an amino acid analogue or amino acid mimetic in which the side chains play no part in ligand-binding.
As used herein , the term capture agent refers to a peptide molecule having a structure such that when a ligand is brought into contact with the capture agent it is bound thereto .
As used herein, the term multimeric capture agent refers to a capture agent comprising at least two linked subunits
As used herein , the term peptide refers to a chain comprising 2 or more amino acid residues, synthetic amino acids, amino acid analogues or amino acid mimetics, or any combination thereof. The term peptide and polypeptide are used interchangeably in this specification .
As used herein , the term substantially enantiomerically pure indicates that the residue comprise s substantially one type of isomer with any other isomeric forms being there only an impurity.
As used herein, the term located in space in a manner favourable to ligand-binding, indicates that the side chains of the peptides which make up the multimeric capture agent are positioned such that they are able to contact and interact with a ligand .
As used herein , the term substantially non hydrophobic means comprising substantially more hydrophilic residues than hydrophobic residues. Example 1
The following series of peptides were synthesised in order to demonstrate peptide self-assembly into an organic solvent layer or onto a hydrophobic surface driven by entropic effects in an aqueous solvent in contact with the said organic solvent layer or hydrophobic surface .
All peptides are labelled with the rhodamine dye TAMRA at the N-terminus . A mixture of the 5-TAM RA and 6-TAMRA isomers was used for the labelling.
Figure imgf000036_0001
In the following, the residue side chains projecting in front of the plane of the paper represent the combinatorially varied 'ligand-binding face'. The residue side chains projecting behind the plane of the paper represent the 'hydrophobic face' (or negative control residues).
In the set of peptides 2DOS-1 to 2DOS-8, a mixture of four side chains (aspartyl, alanyl, seryl, and lysyl) has been used. In the set of peptides 2DOS-9 to 2DOS-16, four hydrophilic (aspartyl) chains have been used.
In the set of peptides 2DOS-1 to 2DOS-4 and the set of peptides 2DOS-9 to 2DOS-12, five residue side chains have been used for the 'hydrophobic face' (or negative control residues). In the set of peptides 2DOS-5 to 2DOS-8 and the set of peptides 2DOS-13 to 2DOS-16, three residue side chains have been used for the 'hydrophobic face' (or negative control residues).
For peptides 2DOS-1, 2DOS-5, 2DOS-9, and 2DOS-13, norleucyl residues have been used for the 'hydrophobic face'. For peptides 2DOS-2, 2DOS-6, 2DOS-10, and 2DOS-14, phenylalanyl residues have been used for the 'hydrophobic face'. For peptides 2DOS-3, 2DOS-7, 2DOS-11, and
2DOS-15, seryl residues have been used as a weak negative control for the 'hydrophobic face'. For peptides 2DOS-4, 2DOS-8, 2DOS-12, and 2DOS-16, aspartyl residues have been used as a strong negative control for the 'hydrophobic face':
Table 1
Figure imgf000037_0001
Figure imgf000038_0001
Figure imgf000039_0001
Peptides were synthesised on a 2 μmol scale using standard FMOC chemistry (Alta Bioscience) and were dissolved to 10 μM in 50% (v/ v) aqueous acetonitrile .
The retention of peptides 2 DOS- 1 to 2 DOS- 16 on a hydrophobic surface (the wells of a polypropylene microtitre plate) was then investigated .
10 mM tris-H Cl (pH 8.0) in 50% (v/ v) aqueous acetonitrile was used as the solvent for the peptides and for TAM RA. 100 μl aliquots of 10 μM peptides 2DOS- 1 to 2DOS- 16 and 10 μM TAMRA were placed in the wells of a Costar microtitre plate as shown in Figure 3.
The microtitre plate was imaged at 200 μm resolution on a Typhoon Trio Plus variable mode imager (Amersham Biosciences) with the green (532 nm) laser and the 580 BP 30 filter at the PMT voltages indicated below and at normal sensitivity. The scan height was set at +3 mm and the sample was pressed during scanning.
The peptides were allowed to evaporate to dryness overnight in the dark and the microtitre plate was again scanned as de scribed above .
The wells were then washed ten time s with 250 μl of water.
The residual surface-bound peptides were finally resuspended in 100 μl of 10 mM tris-HCl (pH 8.0) in 50% (v/ v) aqueous acetonitrile and the microtitre plate was again scanned as described above .
The fluorescence images were analysed using ImageQuant TL v2003.03 (Amersham Biosciences) . The fluorescence images of the microtitre plate scanned at PMT voltages of 600V, 500V, 400V, and 300V at the three stages of the experiment are shown in Figure 4.
Quantification data (using the data from the 400V scan) is given in Table 2 and shown graphically in Figure 5.
Table 2
Figure imgf000042_0001
The results show that phenylalanyl residues lead to greater retention than norleucyl residues. They also show that peptides with five hydrophobic 'anchor residues' are retained better than equivalent peptides with three hydrophobic 'anchor residues'. Changing the
'ligand-binding' residues from aspartyl, alanyl, seryl, and lysyl to a run of four aspartyl residues leads to a drop in retention on the polypropylene surface.
Further experiments were undertaken to investigate the retention of peptides P l - I to P l -5 and P2- 1 to P2-2 , shown in Table 3 , on a polypropylene surface. Table 3
Peptide Sequence
Pl-I TAMRA-F-G-F-S-F-A-F-D-F-G-F
Pl-2 TAMRA-F-G-F-G-F-S-F-A-F-D-F-G-F
Pl-3 TAMRA-F-G-F-G-F-G-F-S-F-A-F-D-F-G-F
Pl-4 TAMRA-F-G-F-G-F-G-F-G-F-S-F-A-F-D-F-G-F
Pl-5 TAMRA-F-G-F-G-F-G-F-G-F-G-F-S-F-A-F-D-F-G-F
P2-1 TAMRA-G-S-F-A-F-D-F
P2-2 TAMRA-G-S-G-A-F-D-F
The polypropylene sheet was wiped with 50% (v/v) aqueous acetonitrile prior to use.
8x replicate 20 nl volumes of 1 μM peptides Pl-I to Pl-5 and P2-1 to P2-2 and TAMRA in dimethyl sulphoxide (DMSO) were dispensed at 1 mm spacing to a 3"xl"xl mm polypropylene sheet using the Piezorray system (PerkinElmer LAS). 500 drops were pre-dispensed using the 'side shoot' option and the tuning was set to 72V for 30μs.
The slide was imaged at 10 μm resolution on a Typhoon Trio Plus variable mode imager (Amersham Biosciences) with the green (532 nm) laser and the 580 BP 30 filter at a PMT voltage of 600 V and at normal sensitivity. The scan height was set at the platen and the samples were pressed during scanning. The fluorescence image was analysed using ImageQuant TL v2003.03 (Amersham Biosciences).
The lower half of the slide (containing the test array) was then washed in 100 ml of 1 M NaCl containing 10 mM tris-HCl (pH 8.0) for one minute and were re-scanned as described above .
The same half of the slide was then washed for a second time in 100 ml of 1 M NaCl containing 10 mM tris- HCl (pH 8.0) for 30 minutes and re-scanned as described above.
The same half of the slide was then washed for a third time in 100 ml of water for 30 minutes and re- scanned as described above .
The fluorescence images for the various arrays are shown in Figure 6A,6B .
The fluorescence values for the various arrayed peptides shown in Figure 6A,6B are shown in Tables 4 - 6 below:
After first wash : Table 4a
Figure imgf000044_0001
Table 4b
Figure imgf000045_0001
After second wash:
Table 5a
Figure imgf000045_0002
Table 5b
Figure imgf000046_0001
After third wash:
Table 6a
Figure imgf000046_0002
Table 6b
Figure imgf000047_0001
These results are shown graphically in Figure 7.
The figures clearly show that there is a gradient of increasing retention for the peptides correlated to increasing peptide chain length . As can be clearly seen , Peptide P l -5 which has a chain length of 19 amino acids has the highest retention.
Example 2
The pH resistance of peptide 2DOS-2 (see above) deposited onto a polypropylene hydrophobic surface was inve stigated :
Twelve 50 μl aliquots of peptide 2 DOS-2 in 10 mM tris-HCl (pH 8.0) in 50% (v / v) aqueous acetonitrile were dried down in the wells of a Costar microtitre plate .
The peptide samples were allowed to evaporate to dryness in the dark.
The dried peptide samples in the first eleven wells were incubated with 200 μl of 100 mM pho sphate buffer for 30 minutes at room temperature according to the scheme shown in Table 7 :
Table 7
Figure imgf000048_0001
All supernatants were pipetted off and the residual surface-bound peptides in all twelve wells were finally resuspended in 50 μl of 10 mM tris-HCl (pH 8.0) in 50% (v/ v) aqueous acetonitrile and the microtitre plate was imaged at 200 μm resolution on a Typhoon Trio Plu s variable mode imager (Amersham Biosciences) with the green (532 nm) laser and the 580 BP 30 filter at the PMT voltages indicated below and at normal sensitivity . The scan height was set at + 3 mm and the sample was pressed during scanning.
The fluorescence images were analysed using ImageQuant TL v2003.03 (Amersham Bioscience s) . Fluorescence images showing the pH resistance of 2 DOS-2 deposited on polypropylene are shown in Figure 8.
Quantification data for peptide 2 DOS-2 retention (using data from the 300V scan) are given in Table 8 and graphically in Figure 9.
Table 8
Figure imgf000049_0001
The results show that the retention of peptide 2DOS-2 on a polypropylene surface is therefore stable over a broad range of pH values, with maximal retention at low and high pH and minimal retention around pH 6.5.
Example 3
The time-dependent persistence of peptide 2 DOS-2 (see above) deposited onto a polypropylene hydrophobic surface in the presence of aqueous buffer was investigated as shown below: Twelve 100 μl aliquots of 5 μM peptide 2 DOS-2 in 5 mM tris- HCl (pH 8.0) in 75% (v / v) aqueous acetonitrile were dispensed to the wells of the top row of a Costar microtitre plate . The peptide samples were allowed to evaporate to dryness in the dark.
The dried peptide samples in wells 1 - 10 were incubated with 250 μl of 1 M NaCl in 1 0 mM tris-H Cl (pH 8.0) for the time indicated below at room temperature . All supernatants were pipetted up and down 8 times after incubation and the supernatants were then removed and placed in the wells of the bottom row of the microtitre plate .
The residual surface-bound peptides in all twelve wells were finally resuspended in 50 μl of 1 0 mM tris-HCl (pH 8.0) in 50% (v/ v) aqueous acetonitrile and the microtitre plates were imaged at 200 μra resolution on a Typhoon Trio Plus variable mode imager (Amersham Biosciences) with the green
(532 nm) laser and the 580 BP 30 filter at the PMT voltages indicated below and at normal sensitivity. The scan height was set at +3 mm and the sample was pressed during scanning.
The fluorescence images were analysed using ImageQuant TL v2003.03 (Amersham Biosciences) .
Fluorescence data for the time-dependent persistence of peptide 2 DOS-2 deposited onto a polypropylene hydrophobic surface in the presence of aqueous buffer are shown in Figure 10.
Quantification data for peptide 2DOS-2 retention (using data from the 300V scan) are shown in Table 9 and Figure 1 1 .
Table 9
Figure imgf000051_0001
The results show that retention of peptide 2DOS-2 on a hydrophobic polypropylene surface is stable for extended periods of time in 1 M NaCl / 10 mM tris-HCl (pH 8.0) .
Example 4
The retention of peptides 2 DOS- 1 to 2 DOS- 16 (see above) on polypropylene wells of different geometries was investigated :
10 mM tris-HCl (pH 8.0) in 50% (v / v) aqueous acetonitrile was used as the solvent for the peptides and for TAMRA. 1 μl aliquots of 10 μM peptides 2 DOS- 1 to 2 DOS- 16 and
10 μM TAMRA were pipetted into the wells of a Costar
V-bottomed polypropylene microtitre plate and a Greiner flat-bottomed polypropylene microtitre plate according to the following scheme as shown in Figure 12 :
The peptide samples were allowed to evaporate to dryness in the dark.
The peptide samples in the top two rows of the microtitre plates were then incubated for 1 5 minutes at room temperature in 250 μl of 1 M NaCl in 10 mM tris-HCl (pH 8.0) .
After incubation , the wash buffer was pipetted up and down eight times in the well before removing the supernatant.
The washed and untreated peptide samples were then resuspended in 50 μl of 10 mM tris-H Cl (pH 8.0) in 50% (v / v) aqueous acetonitrile .
The microtitre plates were imaged at 200 μm resolution on a Typhoon Trio Plus variable mode imager (Amersham Biosciences) with the green (532 nm) laser and the 580 BP 30 filter at the PMT voltages indicated below and at normal sensitivity. The scan height was set at the platen and the sample was pressed during scanning.
The fluorescence images were analysed using ImageQuant TL v2003.03 (Amersham Biosciences) .
The fluorescence images of the plate s scanned at PMT voltages of 600V and 500V are shown in Figure 13. Quantification data for the V-bottom wells (using data from the 500V scan) are shown in Table 10 and Figure 14 :
Table 10
Figure imgf000053_0001
Quantification data for the flat-bottom wells (using data from the 500V scan) are shown in Table 1 1 and Figure 15 : Table 11
Figure imgf000054_0001
The results show that retention of peptides 2DOS-1 to 2DOS-16 on polypropylene wells of different geometries is comparable, indicating that retention is not dependent upon drying down in wells with a V-bottomed geometry.
Example 5
The retention of peptides 2DOS-1 to 2DOS-16 (see above) on polypropylene and polystyrene surfaces was compared:
5 mM tris-HCl (pH 8.0) in 75% (v/v) aqueous acetonitrile was used as the solvent for the peptides and for TAMRA. 20 μl aliquots of 5 μM peptides 2 DOS- 1 to 2 DOS- 16 and 5 μM TAMRA were pipetted into the wells of a Costar V-bottomed polypropylene microtitre plate , a Greiner V-bottomed polypropylene microtitre plate , and a Greiner V-bottomed polystyrene microtitre plate according to the scheme shown in Figure 16:
The peptide samples were allowed to evaporate to dryness in the dark.
The peptide samples in the top two rows of the microtitre plates were then incubated for 1 5 minutes at room temperature in 250 μl of 1 M NaCl in 10 mM tris- HCl (pH 8.0) . After incubation , the wash buffer was pipetted up and down eight times in the well before removing the supernatant.
The washed and untreated peptide samples were then resuspended in 50 μl of 10 mM tris- HCl (pH 8.0) in 50% (v/ v) aqueous acetonitrile .
The microtitre plates were imaged at 200 μm resolution on a Typhoon Trio Plus variable mode imager (Amersham Biosciences) with the green (532 nm) laser and the 580 BP 30 filter at the PMT voltages indicated below and at normal sensitivity. The scan height was set at +3 mm and the sample was pressed during scanning.
The fluorescence images were analysed using ImageQuant TL v2003.03 (Amersham Biosciences) . The fluorescence images of the slide s scanned at PMT voltages of 600V, 500V, and 400V are shown in Figure 1 7 :
Peptide samples in the upper half of the plates have been washed and peptide samples in the lower half of the plates are untreated .
Quantification data for the Costar polypropylene
V-bottom wells (using data from the 400V scan) are given in
Table 12 :
Table 1 2
Figure imgf000056_0001
Quantification data for the Greiner polypropylene V-bottom wells (using data from the 400V scan) are given in Table 13 : Table 13
Figure imgf000057_0001
Quantification data for the Greiner polystyrene V-bottom wells (using data from the 400V scan) are given in Table 14 :
Table 14
Figure imgf000058_0001
These data are shown graphically in Figure 18 :
The results show that comparable peptide behaviour is seen on all three surfaces , demonstrating that retention is a sequence-specific property of the peptides rather than a property that is peculiar to one particular plastic surface .
Example 6
Four peptides were synthesised that contain a 'surface-binding face ' consisting of seven phenylalanyl residues. These peptides also contain a central region consisting of charged and uncharged residues and a variable penultimate residue . The variable penultimate residue was alanyl , seryl , cysteiyl, or nitropyridylthio activated cysteiyl .
An additional four TAM RA-labelled fluorescent peptides were also synthesised that contain an N-terminal TAMRA fluorophore attached to a glycyl residue that is attached to a variable C-terminal residue . The variable C-terminal residue was alanyl, seryl, cysteiyl, or nitropyridylthio activated cysteiyl.
A mixture of the 5-TAMRA and 6-TAMRA isomers as shown in Example 1 was used for the labelling. The full set of eight peptides is shown in Tables 15 and
16 :
Table 15
Figure imgf000060_0001
Table 16
Figure imgf000061_0001
The peptides SB- I to SB-4 and TLSP- I to TLSP-4 were used in order to investigate dimer formation .
Two different protocols were used . In the 'liquid phase ' protocol , The SB peptides were dried down onto a polypropylene surface . The TLSP peptides were then added in aqueous solution prior to washing the wells and assaying for retained fluorescent material.
In the 'co-drying' protocol, The SB peptides were mixed with the TLSP peptide s and both were then dried down together onto a polypropylene surface prior to washing the wells and assaying for retained fluorescent material .
A further protocol in which the SB peptides are mixed with the TLSP peptides in aqueous solution and allowed to react to produce peptide dimers which are then dried down onto a polypropylene surface could easily be achieved by one skilled in the art.
In the 'liquid phase' protocol , 50 μl of 10 μM peptides SB- I to SB-4 in 1 mM NaH2PO4 in 50% (v / v) aqueous acetonitrile were added the wells of a Costar V-bottomed microtitre plate according to the scheme shown in Table 17 :
Table 17
Figure imgf000062_0001
The samples were dried down overnight in the dark.
50 μl of 100 μM peptides TLSP- I to TLSP-4 in 10 mM NaH2PO4 were then added to the wells according to the scheme shown in Table 18 : Table 18
Figure imgf000063_0001
The samples were incubated at room temperature for one hour in the dark . The supernatants were removed and the wells were washed twice with 200 μl of 1 M NaCl in 10 mM tris-HCl (pH 8.0) . 50 μl of 10 mM tris- H Cl (pH 8.0) in 50% (v/ v) aqueous acetonitrile was finally added to the wells .
The microtitre plate was imaged at 200 μm resolution on a Typhoon Trio Plus variable mode imager (Amersham Biosciences) with the green (532 nm) laser and the 580 BP 30 filter at a PMT voltage of 500 V and at normal sensitivity . The scan height was set at +3 mm and the sample was pressed during scanning. The fluorescence image was analysed using ImageQuant TL v2003.03 (Amersham Biosciences) .
In the 'co-drying' protocol, 50 μl of 10 μM peptides SB- I to SB-4 in 1 mM NaH2PO4 in 50% (v / v) aqueous acetonitrile were added to the wells of a Costar V-bottomed microtitre plate according to the scheme shown in Table 19 : Table 19
Figure imgf000064_0001
50 μl of 100 μM peptides TLSP- I to TLSP-4 in 1 mM NaH2PO4 in 50% (v/ v) aqueous acetonitrile were then added to the wells according to the scheme shown in Table 20 :
Table 20
Figure imgf000064_0002
The samples were dried down overnight in the dark.
The wells were then washed twice with 200 μl of 1 M NaCl in 10 mM tris- HCl (pH 8.0) . 50 μl of 10 mM tris-HCl (pH 8.0) in 50% (v/ v) aqueous acetonitrile was finally added to the wells.
The microtitre plate was imaged at 200 μm resolution on a Typhoon Trio Plus variable mode imager (Amersham Biosciences) with the green (532 nm) laser and the 580 BP 30 filter at a PMT voltage of 500 V and at normal sensitivity . The scan height was set at +3 mm and the sample was pressed during scanning. The fluorescence image was analysed using ImageQuant TL v2003.03 (Amersham Biosciences) .
The fluorescence image for the microtitre plate from the experiment using the 'liquid phase ' protocol is shown in Figure 19A.
The fluorescence data for the 'liquid phase ' protocol are given in Table 2 1 : Table 2 1
Figure imgf000065_0001
The results are shown graphically in Figure 19B :
The fluorescence image for the microtitre plate from the experiment using the 'co-drying' protocol is shown in Figure
2OA.
The fluorescence data for the 'co-drying' protocol are given in the following Table 22 : Table 22
Figure imgf000066_0001
The results are shown graphically in Figure 2OB : The yield of dimer is assayed by the retention of fluorescently labelled peptide which is conditional upon the presence of an unlabelled peptide that can bind to both the polypropylene surface and to the fluorescently labelled peptide .
For the 'liquid phase protocol' dimer yields are lower than for the 'co-drying' protocol but the chemical specificity for dimer formation is better. Maximal dimer formation is seen when the surface peptide posse sse s a free thiol group and the solution peptide possesses an S-nitropyridyl activated thiol group . Dimer formation is also observed when the surface peptide possesses an S- nitropyridyl activated thiol group and the solution peptide also possesses an S-nitropyridyl activated thiol group ; when the surface peptide possesses a free thiol group and the solution peptide also possesses a free thiol group; and when the surface peptide possesses an S-nitropyridyl activated thiol group and the solution peptide possesses a free thiol group .
Free thiol coupling to free thiols may be due to simple aerobic oxidation , forming disulfide bonds. S-nitropyridyl activated thiol coupling to S-nitropyridyl activated thiols may be a result of incomplete thiol activation , leaving some free thiols able to react with the remaining S-nitropyridyl activated thiols , or some other mechanism.
Results for the 'co-drying' protocol mirror those described above . Dimer yields are generally higher with this method but non-specific binding is also higher. In particular, some reactivity is observed between a hydroxylated peptide attached to the surface and solution peptides containing both free thiol groups and S-nitropyridyl activated thiol groups .
Example 7 In this example , peptide dimers are fabricated on a planar plastic surface using a Piezorray (PerkinElmer LAS) non-contact dispenser. The Piezorray (PerkinElmer LAS) is specifically designed for pipetting nanolitre volumes to den se arrays. Liquid volumes are controlled by a piezoelectric tip. The Piezorray system contains a source plate holder, an ultrasonic washbowl, a computer and monitor, and a bottle for system liquid.
Polypropylene sheet was obtained from SBA plastics
(http: / / www. sba. co . uk/ , Propylex Natural Polypropylene Sheet 2440 x 1220 x 1 mm) and was wiped with 50% (v/ v) aqueous acetonitrile prior to use . ix 10x 10 arrays of 5nl of l OOμM peptides SB- I and SB-3 in I mM NaH2PO4 in 50% (v / v) aqueous acetonitrile or solvent control were dispensed to 1 mm polypropylene sheet cut to 3"x l " using the Piezorray system according to the scheme shown in Table 23.
Table 23
1 mM NaH2 PO4 in 50% (v/v) aqueous acetonitrile
1 mM NaH2 PO4 in 50% (v/v) aqueous acetonitrile
Peptide SB-I
Peptide SB-I
Peptide SB-3
Peptide SB-3
Six 10x 10 arrays of 5 nl of 100 μM peptide TLSP-4 in either 1 mM NaH2PO4 in 50% (v/ v) aqueous acetonitrile or in 1 mM NaH2PO4 in 50% (v/ v) aqueous acetonitrile and 10% (v/v) glycerol were then dispensed over the previous spots using the Piezorray system according to the scheme shown in Table 24 :
Table 24
Peptide TLSP- 4
Peptide TLSP-4 in 10% glycerol
Peptide TLSP- 4
Peptide TLSP-4 m 10% glycerol
Peptide TLSP- 4
Peptide TLSP-4 in 10% glycerol
The samples were incubated at room temperature for 30 minutes in the dark. The slide was then washed in 100 ml of 50 mM NaCl in 10 mM tris-HCl (pH 8.0) followed by running tap water over the slide for one minute .
The microtitre plate was imaged at 10 μm resolution on a Typhoon Trio Plus variable mode imager (Amersham
Biosciences) with the green (532 nm) laser and the 580 BP 30 filter at a PMT voltage of 400 V and at normal sensitivity.
The scan height was set at the platen and the sample was pressed during scanning. The fluorescence image was analysed using ImageQuant TL v2003.03 (Amersham
Biosciences) .
The fluorescence image for the polypropylene slide is shown in Figure 2 1 :
The yield of dimer is assayed by the retention of fluorescently labelled peptide that is conditional upon the presence of an unlabelled peptide that can bind to both the polypropylene surface and to the fluorescently labelled peptide .
Dimer formation is therefore seen when the surface peptide possesses a free thiol group and the solution peptide possesses an S-nitropyridyl activated thiol group. The simple protocol (without glycerol to prevent evaporation) gives a higher yield of dimer.
Example 8 In this example , twenty 256-element microarrays of dimers comprising peptides Ll-Pl-I to 16 and L1-P2-1 to 16 were fabricated in parallel.
1 mm polypropylene sheet was cut to 136 mm x 80mm, lightly abraded with glass paper, and wiped with 50% (v/v) aqueous acetonitrile prior to use.
18x 6 nl aliquots of Pl peptides were arrayed down the columns of the polypropylene slide at a spacing of 0.72 mm as indicated in Table 25, using the Piezorray system (PerkinElmer LAS).
Table 25
Column Pl peptide Solvent number
1 2 μM Pl-5 90% (v/v) DMSO, 1 mM tris-HCl (pH 8.0)
2 20 μM Ll-Pl-I 90% (v/v) DMSO, 1 mM tris-HCl (pH 8.0), 2 mM TCEP
3 20 μM Ll-Pl-2 90% (v/v) DMSO, 1 mM tris-HCl (pH 8.0), 2 mM TCEP
4 20 μM Ll-Pl-3 90% (v/v) DMSO, 1 mM tris-HCl (pH 8.0), 2 mM TCEP
5 20 μM Ll-Pl-4 90% (v/v) DMSO, 1 mM tris-HCl (pH 8.0) , 2 mM TCEP
6 20 μM Ll-Pl-5 90% (v/v) DMSO, 1 mM tris-HCl (pH 8.0), 2 mM TCEP
7 20 μM Ll-Pl-6 90% (v/v) DMSO, 1 mM tris-HCl (pH 8.0), 2 mM TCEP
8 20 μM Ll-Pl-7 90% (v/v) DMSO, 1 mM tris-HCl (pH 8.0), 2 mM TCEP
9 20 μM Ll-Pl-8 90% (v/v) DMSO, 1 mM tris-HCl (pH 8.0), 2 mM TCEP
10 20 μM Ll-Pl-9 90% (v/v) DMSO, 1 mM tris-HCl (pH 8.0), 2 mM TCEP
11 20 μM Ll-Pl-IO 90% (v/v) DMSO, 1 mM tris-HCl (pH 8.0), 2 mM TCEP
12 20 μM Ll-Pl-Il 90% (v/v) DMSO, 1 mM tris-HCl (pH 8.0), 2 mM TCEP
13 20 μM Ll-Pl-12 90% (v/v) DMSO, 1 mM tris-HCl (pH 8.0), 2 mM TCEP
14 20 μM Ll-Pl-13 90% (v/v) DMSO, 1 mM tris-HCl (pH 8.0) , 2 mM TCEP
15 20 μM Ll-Pl-14 90% (v/v) DMSO, 1 mM tris-HCl (pH 8.0), 2 mM TCEP
16 20 μM Ll-Pl-15 90% (v/v) DMSO, 1 mM tris-HCl (pH 8.0), 2 mM TCEP
17 20 μM Ll-Pl-16 90% (v/v) DMSO, 1 mM tris-HCl (pH 8.0), 2 mM TCEP
18 2 μM Pl-5 90% (v/v) DMSO, 1 mM tris-HCl (pH 8.0)
DMSO = dimethyl sulfoxide
TCEP = tris (2 -carboxyethyl) phosphine Sequence of P l peptides:
P1-5 TAMRA-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Ser-Phe-Ala-Phe-Asp-Phe-Gly-Phe L1-P1-1 Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Cys-Phe-DAB-Phe-DAB-Phe-Gly-Phe L1 -P1 -2 Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Cys-Phe-DAB-Phe-Hse-Phe-Gly-Phe
L1-P1-3 Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Cys-Phe-DAB-Phe-Abu-Phe-Gly-Phe L1-P1-4 Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Cys-Phe-DAB-Phe-Asp-Phe-Gly-Phe L1-P1-5 Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Cys-Phe-Hse-Phe-DAB-Phe-Gly-Phe L1-P1-6 Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Cys-Phe-Hse-Phe-Hse-Phe-Gly-Phe L1 -P1 -7 Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Cys-Phe-Hse-Phe-Abu-Phe-Gly-Phe
L1-P1-8 Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Cys-Phe-Hse-Phe-Asp-Phe-Gly-Phe L1-P1-9 Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Giy-Phe-Cys-Phe-Abu-Phe-DAB-Phe-Gly-Phe L1-P1-10 Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Cys-Phe-Abu-Phe-Hse-Phe-Gly-Phe L1-P1-11 Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Cys-Phe-Abu-Phe-Abu-Phe-Gly-Phe L1-P1-12 Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Cys-Phe-Abu-Phe-Asp-Phe-Gly-Phe
L1-P1-13- Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Cys-Phe-Asp-Phe-DAB-Phe-Gly-Phe L1-P1-14 Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Cys-Phe-Asp-Phe-Hse-Phe-Gly-Phe L1-P1-15 Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Cys-Phe-Asp-Phe-Abυ-Phe-Gly-Phe L1 -P1-16 Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Gly-Phe-Cys-Phe-Asp-Phe-Asp-Phe-Gly-Phe After sample evaporation, 18x 12 nl aliquots of L 1 -P2 peptides in 90% (v / v) DMSO , 1 mM tris-H Cl (pH 8.0) were arrayed along the rows of the polypropylene slide at a spacing of 0.72 mm as indicated in Table 26, using the Piezorray system (PerkinElmer LAS) .
Table 26
Figure imgf000073_0001
Sequence of P2 peptides:
L1-P2-1 CysSTP-DAB-Phe-DAB-Phe-Gly-Phe L1-P2-2 CysSTP-DAB-Phe-Hse-Phe-Gly-Phe L1-P2-3 CysSTP-DAB-Phe-Abu-Phe-Gly-Phe L1-P2-4 CysSTP-DAB-Phe-Asp-Phe-Gly-Phe
L1-P2-5 CysSTP-Hse-Phe-DAB-Phe-Gly-Phe L1-P2-6 CysSTP-Hse-Phe-Hse-Phe-Gly-Phe L1-P2-7 CysSTP-Hse-Phe-Abu-Phe-Gly-Phe L1-P2-8 CysSTP-Hse-Phe-Asp-Phe-Gly-Phe L1-P2-9 CysSTP-Abu-Phe-DAB-Phe-Gly-Phe
L1-P2-10 CysSTP-Abu-Phe-Hse-Phe-Gly-Phe L1-P2-11 CysSTP-Abu-Phe-Abu-Phe-Gly-Phe L1-P2-12 CysSTP-Abu-Phe-Asp-Phe-Gly-Phe L1-P2-13 CysSTP-Asp-Phe-DAB-Phe-Gly-Phe L1-P2-14 CysSTP-Asp-Phe-Hse-Phe-Gly-Phe
L1-P2-15 CysSTP-Asp-Phe-Abu-Phe-Gly-Phe L1-P2-16 CysSTP-Asp-Phe-Asp-Phe-Gly-Phe L1-P2-17 TAMRA-CysSTP-DAB-Phe-DAB-Phe-Gly-Phe L1-P2-18 TAMRA-CysSTP-Hse-Phe-Hse-Phe-Gly-Phe L1-P2-19 TAMRA-CysSTP-Abu-Ph.e-Abu-Phe-Gly-Phe
L1-P2-20 TAMRA-CysSTP-Asp-Phe-Asp-Phe-Gly-Phe After sample evaporation, the slide was washed for 10 minutes in 50 ml of 10 mM tris-HCl (pH 8.0) containing 0.1% (v/v) Tween-20. The slide was imaged at 10 μm resolution on a Typhoon Trio Plus variable mode imager (Amersham Biosciences) with the green (532 nm) laser and the 580 BP 30 filter at a PMT voltage of 500V and at normal sensitivity. The scan height was set at the platen. The fluorescence image was analysed using ImageQuant TL v2003.03 (Amersham Biosciences).
The fluorescence image for one 18x18 array of dimer and control spots is shown in Figure 22.
Fluorescent signal is observable for each Ll-Pl peptide column dispensed to the array. This indicates that each of the Ll-Pl peptides has been successfully dispensed, and is capable of dimer formation. The fluorescent signal is also observable for each L1-P2 peptide row dispensed to the array.
This indicates that each of the L1-P2 peptides has been successfully dispensed, and is capable of dimer formation. The dimer fluorescence is greater for the samples with only TAMRA-labelled P2 peptides compared to the dimer fluorescence for the 16x16 array fabricated with both unlabelled P2 peptides and TAMRA-labelled P2 peptides competing for the Ll-Pl peptide thiol groups. This indicates that all of the L1-P2 peptides have successfully competed with their TAMRA-labelled counterparts and have therefore successfully formed peptide dimers between all sixteen Ll-Pl peptides and all sixteen L1-P2 peptides.
The invention being thus described, it will be obvious that the same way may be varied in many ways. Such variations are not to be regarded as a departure from the spirit and scope of the invention, and all such modifications as would be obvious to one skilled in the art are intended to be included within the scope of the following claims .
I NDUSTRIAL APPLICABI LITY
The current invention provides synthetic capture agents having increased sequence diversity. The capture agents can functionalize various surfaces , for example , glass or silicon, so as to allow the binding of ligands to the surface , or to form arrays of various types. l

Claims

1 . A method of functionalising a substrate comprising immobilising at least one multimeric peptide on said substrate, wherein, the at least one multimeric peptide comprises at least first and second peptide chains, said first peptide chain comprising at least one hydrophobic amino acid residue and at least one functionalising moiety, wherein the at least one hydrophobic amino acid residue and at least one functionalising moiety are positioned in the peptide primary structure so as to result in a hydrophobic face, and a substantially non hydrophobic face comprising the functionalising moiety, and wherein , contacting the peptide with the substrate causes the peptide to be immobilised thereon.
2. The method according to claim 1 wherein, the substrate is a hydrophobic substrate.
3. The method according to claim 1 wherein, the substrate is coated in a hydrophobic layer.
4. The method according to any one of claims 1 to 3 wherein, the first peptide chain is immobilised on the substrate by a hydrophobic interaction between the substrate and the hydrophobic face of the peptide.
5. The method according to any preceding claim wherein, the hydrophobic amino acids whose side chains form
5 the hydrophobic face are selected from the group consisting of leucine, isoleucine, norleucine, valine, norvaline, methionine, tyrosine, tryptophan and phenylalanine.
6. The method according to any preceding claim 10 wherein, the hydrophobic amino acids are phenylalanine.
7. The method according to any preceding claim wherein, each hydrophobic amino acid monomer is substantially enantiomerically pure.
L5
8. The method according to any preceding claim wherein, the functionalising moiety comprises at least one amino acid selected from the group comprising L-amino acids, D-amino acids, amino acid mimetics, spacer amino acids, beta 0 amino acids, or any other chiral amino acid monomers.
9. The method according to any preceding claim wherein, each amino acid monomer which forms the functionalising moiety is substantially enantiomerically pure.
10. The method according to any preceding claim wherein , the first peptide chain comprises a primary structure comprising alternating hydrophobic and substantially non hydrophobic amino acid residues .
1 1 . The method according to any preceding claim wherein , the first peptide chain comprises between 20% and 80% hydrophobic amino acid residues.
12. The method according to any preceding claim wherein , the functionalising moiety comprises 10 or fewer amino acid residues .
13. The method according to any preceding claim wherein , the multimeric peptide comprises a peptide dimer comprising first and second peptide chains.
14. The method according to any preceding claim wherein , the peptide dimer is assembled on the hydrophobic substrate .
15. The method according to claim 13 or 14 wherein, the second peptide chain also comprises at least one hydrophobic amino acid residue and at least one non hydrophobic amino acid residue, wherein said amino acids are positioned in the peptide primary structure such that the amino acid side chains are located to produce a hydrophobic face and a substantially non hydrophobic face comprising the functionalising moiety.
16. The method according to any one of claims 13 to 1 5 wherein , the second peptide chain comprises fewer amino acids than the first peptide chain .
17. The method according to any one of claims 1 3 to 16 wherein , the second peptide chain comprises 1 -6 hydrophobic amino acid residues .
18. The method according to any one of claims 13 to 17 wherein , the second peptide chain contains 10 or fewer amino acid residues forming the functionalising moiety.
19. The method according to any one of claims 1 3 to 18 wherein , the first and second peptide chains each contain at least one reactive group .
20. The method according to claim 19 wherein , the reactive group on the first peptide chain is located in the primary amino acid structure on the substantially non hydrophobic face and to the N-terminal side of the functionalising moiety and in the second peptide chain , in the hydrophobic face and to the N-terminal side of the functionalising moiety.
2 1 . The method according to claim 19 or 20 wherein , said reactive groups are selected from the set consisting of thiol groups, maleimide , cyclopentadiene , azide , phosphinothioesters , thioesters and (nitro) thiopyridyl activated thiols .
22. The method according to claim 2 1 wherein , the thiol group is activated with either a thionitropyridyl or thiopyridyl group .
23. The method according to any preceding claim wherein , the functionalising moiety allows a ligand to bind to the immobilised peptide .
24. A substrate functionalised according to the method of any one of claims 1 to 23.
25. An array comprising a substrate functionalised according to the method of any one of claims 1 to 23 wherein , said array compri ses multiple immobilised peptides .
26. The array according to claim 25 comprising a number of discrete addressable spatially encoded loci.
27. The array according to claim 25 or 26 wherein , substantially all of said peptides at a given locus on the array are substantially the same .
28. The array according to any one of claims 25 to 27 wherein , each locus on the array comprises a different immobilised peptide .
29. A capture agent for binding a ligand, comprising at least first and second peptides, the first peptide comprising at least one hydrophobic amino acid residues and at least one ligand-binding moiety, wherein the at least one hydrophobic amino acid residue and at least one ligand-binding moiety are positioned in the peptide primary structure such that the first peptide comprises a hydrophobic face , and a substantially non hydrophobic ligand- binding face.
30. The capture agent according to claim 29 , wherein , the first peptide comprises 6 to 12 hydrophobic amino acid residues .
3 1 . The capture agent according to claim 29 or 30 , wherein the ligand-binding moiety is selected from the set consisting of hydroxyl groups, thiol groups, carboxylic acids groups, amino groups, amide groups , guanidinium groups, imidazole groups, aromatic groups , chromophores , fluorophores, isotopic labels, chelating groups, haptens , and biotin.
32. The capture agent according to any one of claim 29 to 3 1 wherein, the ligand-binding moiety comprises at least one amino acid.
33. The capture agent according to any one of claims 29 to claim 32 , wherein each amino acid positioned so as to be located on the ligand-binding face is selected from a set consisting of less than 6 amino acids.
34. The capture agent according to any one of claims 29 to 33 , wherein the first peptide comprises a primary structure comprising alternating hydrophobic and non hydrophobic amino acid residues.
35. The capture agent according to any one of claims 29 to claim 34 , wherein the first peptide comprises between 20% and 80% hydrophobic amino acid residues.
36. The capture agent according to any one of claims 29 to claim 35 , wherein the hydrophobic amino acids which form the hydrophobic face are selected from the group consisting of leucine , isoleucine , norleucine, valine , norvaline , methionine , tyrosine, tryptophan and phenylalanine .
37. The capture agent according to any one of claims 29 to claim 36 , wherein the hydrophobic amino acids present on the hydrophobic face are phenylalanine .
38. The capture agent according to any one of claims 29 to 37 , wherein the second peptide comprises at least one hydrophobic amino acid residue and at least one non hydrophobic amino acid residue , wherein said amino acids are positioned in the peptide primary structure such that the amino acid side chains are located in space to produce a hydrophobic face and a substantially non hydrophobic ligand-binding face .
39. The capture agent according to any one of claims
29 to 38 , wherein the second peptide comprises a chain of fewer amino acids than the first peptide .
40. The capture agent according to any one of claims 29 to 39 , wherein the second peptide comprises fewer hydrophobic residues than the first peptide .
4 1 . The capture agent according to any one of claims 29 to 40 wherein , the second peptide comprises 1 -6 hydrophobic amino acid residues .
42. The capture agent according to any one of claims 29 to 4 1 , wherein the first peptide comprises 10 or fewer ligand-binding residues located on the substantially non hydrophobic ligand-binding face .
43. The capture agent according to any one of claims 29 to 42 , wherein the second peptide comprises 10 or fewer ligand-binding residues located on the substantially non hydrophobic ligand-binding face .
44. The capture agent according to any one of claims 29 to claim 43 , wherein the capture agent is bound to a substrate such that the substantially non hydrophobic ligand-binding face is accessible for ligand binding.
45. The capture agent according to claim 44, wherein the substrate is a hydrophobic substrate .
46. The capture agent according to claim 45 , wherein the capture agent is attached to the hydrophobic substrate by a hydrophobic interaction .
47. The capture agent according to claim 45 or 46 , wherein the hydrophobic substrate is selected from gold modified by hydrophobic organic thiol treatment, glass modified by surface treatment, or plastic .
48. The capture agent according to any one of claims 44 to 47 , wherein the peptide dimer is assembled on the substrate .
49. The capture agent according to any one of claim 29 to 48 , wherein said first and second peptides each contain at least one reactive group.
50. The capture agent according to claim 49 , wherein the reactive group on the first peptide is located in the primary amino acid structure on the substantially non hydrophobic ligand-binding face and to the N-terminal side of the ligand-binding site and in the second peptide , on the hydrophobic face and to the N-terminal side of the ligand-binding site .
5 1 . The capture agent according to claim 49 or 50 , wherein the reactive groups are selected from the set consisting of thiol, maleimide , cyclopentadiene , azide , phosphinothioesters, thioesters and (nitro) thiopyridyl activated thiols.
52. The capture agent according to claim 5 1 , wherein the reactive groups are thiol groups.
53. The capture agent according to claim 52 , wherein at least one thiol group is an activated thiol.
54. The capture agent according to claim 53 , wherein the thiol group is activated with either a thionitropyridyl or thiopyridyl group .
55. The capture agent according to any one of claim 29 to 54 , wherein the first peptide has the sequence set out in SEQ I D No 1 .
56. The capture agent according to any one of claim 29 to 54 , wherein the second peptide has the sequence set out in SEQ I D No 2.
57. A substrate upon which is immobilised at least one capture agent according to any one of claims 29 to 56.
58. An array comprising a capture agent according to any one of claims 29 to 56.
59. The array of claim 58 , wherein the array comprises a number of discrete addressable spatially encoded loci .
60. The array of claim 58 or claim 59 , wherein substantially all of said capture agents at a given locus on the array are substantially the same .
61 . The array of claim 60 , wherein each locus on the array comprises a different capture agent.
62. A method of identifying a multimeric capture agent which binds to a ligand of interest, said method comprising producing an array of combinatorial capture agents according to any one of claims 29 to 56 , contacting the ligand of interest with the array, and identifying to which capture agent the ligand binds .
63. The method according to claim 62 , wherein the ligand is selected from the set comprising eukaryotic cells, prokaryotic cells , viruses and bacteriophages , prions, spores, pollen grains, allergens , nucleic acids, proteins, peptide s, carbohydrates, lipids, organic compounds, and inorganic compounds.
64. The method according to claim 62 or claim 63, wherein the ligand is a physiological or pharmacological metabolite.
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